Interpreting short tandem repeat variations in humans using mutational constraint

PubMed Central

Gymrek, Melissa; Willems, Thomas; Reich, David; Erlich, Yaniv

2017-01-01

Identifying regions of the genome that are depleted of mutations can reveal potentially deleterious variants. Short tandem repeats (STRs), also known as microsatellites, are among the largest contributors of de novo mutations in humans. However, per-locus studies of STR mutations have been limited to highly ascertained panels of several dozen loci. Here, we harnessed bioinformatics tools and a novel analytical framework to estimate mutation parameters for each STR in the human genome by correlating STR genotypes with local sequence heterozygosity. We applied our method to obtain robust estimates of the impact of local sequence features on mutation parameters and used this to create a framework for measuring constraint at STRs by comparing observed vs. expected mutation rates. Constraint scores identified known pathogenic variants with early onset effects. Our metric will provide a valuable tool for prioritizing pathogenic STRs in medical genetics studies. PMID:28892063

Highly Effective DNA Extraction Method for Nuclear Short Tandem Repeat Testing of Skeletal Remains from Mass Graves

PubMed Central

Davoren, Jon; Vanek, Daniel; Konjhodzić, Rijad; Crews, John; Huffine, Edwin; Parsons, Thomas J.

2007-01-01

Aim To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves. Methods DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit. Results DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles. Conclusions The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method. PMID:17696302

Combining two-directional synthesis and tandem reactions. Part 21: Exploitation of a dimeric macrocycle for chain terminus differentiation and synthesis of an sp(3)-rich library.

PubMed

Storr, Thomas E; Cully, Sarah J; Rawling, Michael J; Lewis, William; Hamza, Daniel; Jones, Geraint; Stockman, Robert A

2015-06-01

The application of a tandem condensation/cyclisation/[3+2]-cycloaddition/elimination reaction gives an sp(3)-rich tricyclic pyrazoline scaffold with two ethyl esters in a single step from a simple linear starting material. The successive hydrolysis and cyclisation (with Boc anhydride) of these 3-dimensional architectures, generates unprecedented 16-membered macrocyclic bisanhydrides (characterised by XRD). Selective amidations could then be achieved by ring opening with a primary amine followed by HATU-promoted amide coupling to yield an sp(3)-rich natural product-like library. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time

PubMed Central

Zhivotovsky, Lev A.; Underhill, Peter A.; Cinnioğlu, Cengiz; Kayser, Manfred; Morar, Bharti; Kivisild, Toomas; Scozzari, Rosaria; Cruciani, Fulvio; Destro-Bisol, Giovanni; Spedini, Gabriella; Chambers, Geoffrey K.; Herrera, Rene J.; Yong, Kiau Kiun; Gresham, David; Tournev, Ivailo; Feldman, Marcus W.; Kalaydjieva, Luba

2004-01-01

We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9×10-4 per 25 years, with a standard deviation across loci of 5.7×10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria. PMID:14691732

Rapid carrier screening using short tandem repeats in the phenylalanine hydroxylase gene.

PubMed

Shawky, R M; el-Aleem, K A; Rifaat, M M; el-Naggar, R L; Marzouk, G M

2002-01-01

Phenylketonuria (PKU) is an autosomal recessive genetic disorder caused by defects in the phenylalanine hydroxylase (PAH) system. Our work aimed to screen the PAH locus for the presence of potentially useful short tandem repeats (STR) as markers for carrier detection in PKU families in Egypt, and to determine the level of PAH heterozygosity within the Egyptian population. The system contains at least eight independent alleles in the Egyptian population, transmitted in a Mendelian fashion. Variations in the number of STR in the 16 families studied gave rise to polymorphisms that proved to be suitable markers for PKU carrier detection and prenatal diagnosis. The most frequent allelic fragment size in PKU patients was 246 bp (35.7%), which together with a fragment of 254 bp accounted for 60.7% of the mutant chromosomes.

Knockdown of Rice microRNA166 by Short Tandem Target Mimic (STTM).

PubMed

Teotia, Sachin; Zhang, Dabing; Tang, Guiliang

2017-01-01

Small RNAs, including microRNAs (miRNAs), are abundant in plants and play key roles in controlling plant development and physiology. miRNAs regulate the expression of the target genes involved in key plant processes. Due to functional redundancy among miRNA family members in plants, an ideal approach to silence the expression of all members simultaneously, for their functional characterization, is desirable. Target mimic (TM) was the first approach to achieve this goal. Short tandem target mimic (STTM) is a potent approach complementing TM for silencing miRNAs in plants. STTMs have been successfully used in dicots to block miRNA functions. Here, we describe in detail the protocol for designing STTM construct to block miRNA functions in rice. Such approach can be applied to silence miRNAs in other monocots as well.

Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

PubMed

Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

2015-09-01

The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA.

PubMed

Gutiérrez, Irene; Garavís, Miguel; de Lorenzo, Sara; Villasante, Alfredo; González, Carlos; Arias-Gonzalez, J Ricardo

2018-05-17

TERRA is an RNA molecule transcribed from human subtelomeric regions toward chromosome ends potentially involved in regulation of heterochromatin stability, semiconservative replication, and telomerase inhibition, among others. TERRA contains tandem repeats of the sequence GGGUUA, with a strong tendency to fold into a four-stranded arrangement known as a parallel G-quadruplex. Here, we demonstrate by using single-molecule force spectroscopy that this potential is limited by the inherent capacity of RNA to self-associate randomly and further condense into entropically more favorable structures. We stretched RNA constructions with more than four and less than eight hexanucleotide repeats, thus unable to form several G-quadruplexes in tandem, flanked by non-G-rich overhangs of random sequence by optical tweezers on a one by one basis. We found that condensed RNA stochastically blocks G-quadruplex folding pathways with a near 20% probability, a behavior that is not found in DNA analogous molecules.

Tandem application of ligand-based virtual screening and G4-OAS assay to identify novel G-quadruplex-targeting chemotypes.

PubMed

Musumeci, Domenica; Amato, Jussara; Zizza, Pasquale; Platella, Chiara; Cosconati, Sandro; Cingolani, Chiara; Biroccio, Annamaria; Novellino, Ettore; Randazzo, Antonio; Giancola, Concetta; Pagano, Bruno; Montesarchio, Daniela

2017-05-01

G-quadruplex (G4) structures are key elements in the regulation of cancer cell proliferation and their targeting is deemed to be a promising strategy in anticancer therapy. A tandem application of ligand-based virtual screening (VS) calculations together with the experimental G-quadruplex on Oligo Affinity Support (G4-OAS) assay was employed to discover novel G4-targeting compounds. The interaction of the selected compounds with the investigated G4 in solution was analysed through a series of biophysical techniques and their biological activity investigated by immunofluorescence and MTT assays. A focused library of 60 small molecules, designed as putative G4 groove binders, was identified through the VS. The G4-OAS experimental screening led to the selection of 7 ligands effectively interacting with the G4-forming human telomeric DNA. Evaluation of the biological activity of the selected compounds showed that 3 ligands of this sub-library induced a marked telomere-localized DNA damage response in human tumour cells. The combined application of virtual and experimental screening tools proved to be a successful strategy to identify new bioactive chemotypes able to target the telomeric G4 DNA. These compounds may represent useful leads for the development of more potent and selective G4 ligands. Expanding the repertoire of the available G4-targeting chemotypes with improved physico-chemical features, in particular aiming at the discovery of novel, selective G4 telomeric ligands, can help in developing effective anti-cancer drugs with fewer side effects. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio. Copyright © 2017 Elsevier B.V. All rights reserved.

Fingerprinting of Cyanobacteria Based on PCR with Primers Derived from Short and Long Tandemly Repeated Repetitive Sequences

PubMed Central

Rasmussen, Ulla; Svenning, Mette M.

1998-01-01

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained. PMID:16349487

Controlling the prion propensity of glutamine/asparagine-rich proteins.

PubMed

Paul, Kacy R; Ross, Eric D

2015-01-01

The yeast Saccharomyces cerevisiae can harbor a number of distinct prions. Most of the yeast prion proteins contain a glutamine/asparagine (Q/N) rich region that drives prion formation. Prion-like domains, defined as regions with high compositional similarity to yeast prion domains, are common in eukaryotic proteomes, and mutations in various human proteins containing prion-like domains have been linked to degenerative diseases, including amyotrophic lateral sclerosis. Here, we discuss a recent study in which we utilized two strategies to generate prion activity in non-prion Q/N-rich domains. First, we made targeted mutations in four non-prion Q/N-rich domains, replacing predicted prion-inhibiting amino acids with prion-promoting amino acids. All four mutants formed foci when expressed in yeast, and two acquired bona fide prion activity. Prion activity could be generated with as few as two mutations, suggesting that many non-prion Q/N-rich proteins may be just a small number of mutations from acquiring aggregation or prion activity. Second, we created tandem repeats of short prion-prone segments, and observed length-dependent prion activity. These studies demonstrate the considerable progress that has been made in understanding the sequence basis for aggregation of prion and prion-like domains, and suggest possible mechanisms by which new prion domains could evolve.

G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction

PubMed Central

Zhang, Bo; Wu, Wen-Qiang; Liu, Na-Nv; Duan, Xiao-Lei; Li, Ming; Dou, Shuo-Xing; Hou, Xi-Miao; Xi, Xu-Guang

2016-01-01

Alternative DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by G-rich sequences that are widely distributed throughout the human genome. We have previously shown that Pif1p not only unfolds G4, but also unwinds the downstream duplex DNA in a G4-stimulated manner. In the present study, we further characterized the G4-stimulated duplex DNA unwinding phenomenon by means of single-molecule fluorescence resonance energy transfer. It was found that Pif1p did not unwind the partial duplex DNA immediately after unfolding the upstream G4 structure, but rather, it would dwell at the ss/dsDNA junction with a ‘waiting time’. Further studies revealed that the waiting time was in fact related to a protein dimerization process that was sensitive to ssDNA sequence and would become rapid if the sequence is G-rich. Furthermore, we identified that the G-rich sequence, as the G4 structure, equally stimulates duplex DNA unwinding. The present work sheds new light on the molecular mechanism by which G4-unwinding helicase Pif1p resolves physiological G4/duplex DNA structures in cells. PMID:27471032

Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

PubMed

Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

2014-01-29

We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.

Transferability of short tandem repeat markers for two wild Canid species inhabiting the Brazilian Cerrado.

PubMed

Rodrigues, F M; Telles, M P C; Resende, L V; Soares, T N; Diniz-Filho, J A F; Jácomo, A T A; Silveira, L

2006-12-13

The maned wolf (Chrysocyon brachyurus) and the crab-eating fox (Cerdocyon thous) are two wild-canid species found in the Brazilian Cerrado. We tested cross-amplification and transferability of 29 short tandem repeat primers originally developed for cattle and domestic dogs and cats on 38 individuals of each of these two species, collected in the Emas National Park, which is the largest national park in the Cerrado region. Six of these primers were successfully transferred (CSSM-038, PEZ-05, PEZ-12, LOCO-13, LOCO-15, and PEZ-20); five of which were found to be polymorphic. Genetic parameter values (number of alleles per locus, observed and expected heterozygosities, and fixation indices) were within the expected range reported for canid populations worldwide.

Monolithic Parallel Tandem Organic Photovoltaic Cell with Transparent Carbon Nanotube Interlayer

NASA Technical Reports Server (NTRS)

Tanaka, S.; Mielczarek, K.; Ovalle-Robles, R.; Wang, B.; Hsu, D.; Zakhidov, A. A.

2009-01-01

We demonstrate an organic photovoltaic cell with a monolithic tandem structure in parallel connection. Transparent multiwalled carbon nanotube sheets are used as an interlayer anode electrode for this parallel tandem. The characteristics of front and back cells are measured independently. The short circuit current density of the parallel tandem cell is larger than the currents of each individual cell. The wavelength dependence of photocurrent for the parallel tandem cell shows the superposition spectrum of the two spectral sensitivities of the front and back cells. The monolithic three-electrode photovoltaic cell indeed operates as a parallel tandem with improved efficiency.

Single-cell forensic short tandem repeat typing within microfluidic droplets.

PubMed

Geng, Tao; Novak, Richard; Mathies, Richard A

2014-01-07

A short tandem repeat (STR) typing method is developed for forensic identification of individual cells. In our strategy, monodisperse 1.5 nL agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet polymerase chain reaction (PCR) is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto the coencapsulated microbeads. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis (CE) STR fragment size analysis. The 9-plex STR profiles of single cells from both pure and mixed populations of GM09947 and GM09948 human lymphoid cells show that all alleles are correctly called and allelic drop-in/drop-out is not observed. The cell mixture study exhibits a good linear relationship between the observed and input cell ratios in the range of 1:1 to 10:1. Additionally, the STR profile of GM09947 cells could be deduced even in the presence of a high concentration of cell-free contaminating 9948 genomic DNA. Our method will be valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low-concentration samples.

Controlling the prion propensity of glutamine/asparagine-rich proteins

PubMed Central

Paul, Kacy R; Ross, Eric D

2015-01-01

ABSTRACT The yeast Saccharomyces cerevisiae can harbor a number of distinct prions. Most of the yeast prion proteins contain a glutamine/asparagine (Q/N) rich region that drives prion formation. Prion-like domains, defined as regions with high compositional similarity to yeast prion domains, are common in eukaryotic proteomes, and mutations in various human proteins containing prion-like domains have been linked to degenerative diseases, including amyotrophic lateral sclerosis. Here, we discuss a recent study in which we utilized two strategies to generate prion activity in non-prion Q/N-rich domains. First, we made targeted mutations in four non-prion Q/N-rich domains, replacing predicted prion-inhibiting amino acids with prion-promoting amino acids. All four mutants formed foci when expressed in yeast, and two acquired bona fide prion activity. Prion activity could be generated with as few as two mutations, suggesting that many non-prion Q/N-rich proteins may be just a small number of mutations from acquiring aggregation or prion activity. Second, we created tandem repeats of short prion-prone segments, and observed length-dependent prion activity. These studies demonstrate the considerable progress that has been made in understanding the sequence basis for aggregation of prion and prion-like domains, and suggest possible mechanisms by which new prion domains could evolve. PMID:26555096

Multifunctional G-Rich and RRM-Containing Domains of TbRGG2 Perform Separate yet Essential Functions in Trypanosome RNA Editing

PubMed Central

Foda, Bardees M.; Downey, Kurtis M.; Fisk, John C.

2012-01-01

Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3′-to-5′ progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain. PMID:22798390

Solar-to-Chemical Energy Conversion with Photoelectrochemical Tandem Cells.

PubMed

Sivula, Kevin

2013-01-01

Efficiently and inexpensively converting solar energy into chemical fuels is an important goal towards a sustainable energy economy. An integrated tandem cell approach could reasonably convert over 20% of the sun's energy directly into chemical fuels like H2 via water splitting. Many different systems have been investigated using various combinations of photovoltaic cells and photoelectrodes, but in order to be economically competitive with the production of H2 from fossil fuels, a practical water splitting tandem cell must optimize cost, longevity and performance. In this short review, the practical aspects of solar fuel production are considered from the perspective of a semiconductor-based tandem cell and the latest advances with a very promising technology - metal oxide photoelectrochemical tandem cells - are presented.

Analysis of an "off-ladder" allele at the Penta D short tandem repeat locus.

PubMed

Yang, Y L; Wang, J G; Wang, D X; Zhang, W Y; Liu, X J; Cao, J; Yang, S L

2015-11-25

Kinship testing of a father and his son from Guangxi, China, the location of the Zhuang minority people, was performed using the PowerPlex® 18D System with a short tandem repeat typing kit. The results indicated that both the father and his son had an off-ladder allele at the Penta D locus, with a genetic size larger than that of the maximal standard allelic ladder. To further identify this locus, monogenic amplification, gene cloning, and genetic sequencing were performed. Sequencing analysis demonstrated that the fragment size of the Penta D-OL locus was 469 bp and the core sequence was [AAAGA]21, also called Penta D-21. The rare Penta D-21 allele was found to be distributed among the Zhuang population from the Guangxi Zhuang Autonomous Region of China; therefore, this study improved the range of DNA data available for this locus and enhanced our ability for individual identification of gene loci.

Assessing rare earth elements in quartz rich geological samples.

PubMed

Santoro, A; Thoss, V; Ribeiro Guevara, S; Urgast, D; Raab, A; Mastrolitti, S; Feldmann, J

2016-01-01

Sodium peroxide (Na2O2) fusion coupled to Inductively Coupled Plasma Tandem Mass Spectrometry (ICP-MS/MS) measurements was used to rapidly screen quartz-rich geological samples for rare earth element (REE) content. The method accuracy was checked with a geological reference material and Instrumental Neutron Activation Analysis (INAA) measurements. The used mass-mode combinations presented accurate results (only exception being (157)Gd in He gas mode) with recovery of the geological reference material QLO-1 between 80% and 98% (lower values for Lu, Nd and Sm) and in general comparable to INAA measurements. Low limits of detection for all elements were achieved, generally below 10 pg g(-1), as well as measurement repeatability below 15%. Overall, the Na2O2/ICP-MS/MS method proved to be a suitable lab-based method to quickly and accurately screen rock samples originating from quartz-rich geological areas for rare earth element content; particularly useful if checking commercial viability. Copyright © 2015 Elsevier Ltd. All rights reserved.

Revisiting the Roco G-protein cycle.

PubMed

Terheyden, Susanne; Ho, Franz Y; Gilsbach, Bernd K; Wittinghofer, Alfred; Kortholt, Arjan

2015-01-01

Mutations in leucine-rich-repeat kinase 2 (LRRK2) are the most frequent cause of late-onset Parkinson's disease (PD). LRRK2 belongs to the Roco family of proteins which share a conserved Ras-like G-domain (Roc) and a C-terminal of Roc (COR) domain tandem. The nucleotide state of small G-proteins is strictly controlled by guanine-nucleotide-exchange factors (GEFs) and GTPase-activating proteins (GAPs). Because of contradictory structural and biochemical data, the regulatory mechanism of the LRRK2 Roc G-domain and the RocCOR tandem is still under debate. In the present study, we solved the first nucleotide-bound Roc structure and used LRRK2 and bacterial Roco proteins to characterize the RocCOR function in more detail. Nucleotide binding induces a drastic structural change in the Roc/COR domain interface, a region strongly implicated in patients with an LRRK2 mutation. Our data confirm previous assumptions that the C-terminal subdomain of COR functions as a dimerization device. We show that the dimer formation is independent of nucleotide. The affinity for GDP/GTP is in the micromolar range, the result of which is high dissociation rates in the s-1 range. Thus Roco proteins are unlikely to need GEFs to achieve activation. Monomeric LRRK2 and Roco G-domains have a similar low GTPase activity to small G-proteins. We show that GTPase activity in bacterial Roco is stimulated by the nucleotide-dependent dimerization of the G-domain within the complex. We thus propose that the Roco proteins do not require GAPs to stimulate GTP hydrolysis but stimulate each other by one monomer completing the catalytic machinery of the other.

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

PubMed

Liu, Xiaowen; Dekker, Lennard J M; Wu, Si; Vanduijn, Martijn M; Luider, Theo M; Tolić, Nikola; Kou, Qiang; Dvorkin, Mikhail; Alexandrova, Sonya; Vyatkina, Kira; Paša-Tolić, Ljiljana; Pevzner, Pavel A

2014-07-03

There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.

Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats.

PubMed

Seman, Ali; Sapawi, Azizian Mohd; Salleh, Mohd Zaki

2015-06-01

Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84-1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data.

A serum and platelet-rich plasma serotonin assay using liquid chromatography tandem mass spectrometry for monitoring of neuroendocrine tumor patients.

PubMed

Korse, Catharina M; Buning-Kager, Johanna C G M; Linders, Theodora C; Heijboer, Annemieke C; van den Broek, Daan; Tesselaar, Margot E T; van Tellingen, Olaf; van Rossum, Huub H

2017-06-01

Serotonin is used for the diagnosis and follow-up of neuroendocrine tumors (NET). We describe the analytical and clinical validation of a liquid chromatography tandem mass spectrometry (LC-MS/MS) based serotonin assay for serum and platelet-rich plasma (PRP). An LC-MS/MS based method for serum and PRP serotonin was validated by determination of assay imprecision, carry-over, linearity, interference, recovery, sample stability and a matrix/method comparison of serum and PRP serotonin was made with whole blood serotonin. Furthermore, upper limits of normal were determined and serotonin concentrations of healthy individuals, 14 NET patients without evidence of disease and 51 NET patients with evidence of disease were compared. For serum and PRP fractions, total assay imprecision was <5%. All correlation coefficients were 0.98 and the serum and platelet-rich serotonin upper limit of normal were 5.5nmol/10 9 platelet and 5.1nmol/10 9 platelet, respectively. NET patients with confirmed evidence of disease had significantly higher serum and PRP serotonin levels when compared to NET patients without evidence of disease and healthy volunteers. LC-MS/MS based serum and PRP serotonin assays were developed with suitable analytical characteristics. Furthermore, serum and PRP serotonin was found to be useful for monitoring NET patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic diversity of Y-short tandem repeats in Chinese native cattle breeds.

PubMed

Xin, Y P; Zan, L S; Liu, Y F; Tian, W Q; Wang, H B; Cheng, G; Li, A N; Yang, W C

2014-11-14

The aim of this study is to use Y-chromosome gene polymorphism method to investigate regional differences in genetic variation and population evolution history of the Chinese native cattle breeds. Six Y-chromosome short tandem repeat (Y-STR) loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404, and UMN0103) were analyzed using 1016 healthy and heterogenetic males and 90 females of 9 native cattle breeds (Qinchuan, Jinnan, Zaosheng, Luxi, Nanyang, Jiaxian, Dabieshan, Yanbian, and Menggu) in China. Allele frequency and gene diversity were calculated for the various populations. The results indicated that Y-STRs in the 6 loci have polymorphisms and genetic diversity in Chinese cattle populations. The genetic diversity analysis revealed that the Chinese cattle populations have a close genetic relationship. The analysis of INRA124, UMN2404, and UMN0103 loci revealed the original history of Chinese cattle because of which cattle belonging to Bos taurus or Bos indicus could be determined. Interestingly, a declining zebu introgression was displayed from South to North and from East to West in the Chinese geographical distribution, which implied that cattle population from various regions of China had been subjected to somewhat different evolutionary history. This conclusion supported other evidences such as earlier archaeological, historical research, and blood protein polymorphism analysis.

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa.

PubMed

Erkek, Serap; Hisano, Mizue; Liang, Ching-Yeu; Gill, Mark; Murr, Rabih; Dieker, Jürgen; Schübeler, Dirk; van der Vlag, Johan; Stadler, Michael B; Peters, Antoine H F M

2013-07-01

In mammalian spermatozoa, most but not all of the genome is densely packaged by protamines. Here we reveal the molecular logic underlying the retention of nucleosomes in mouse spermatozoa, which contain only 1% residual histones. We observe high enrichment throughout the genome of nucleosomes at CpG-rich sequences that lack DNA methylation. Residual nucleosomes are largely composed of the histone H3.3 variant and are trimethylated at Lys4 of histone H3 (H3K4me3). Canonical H3.1 and H3.2 histones are also enriched at CpG-rich promoters marked by Polycomb-mediated H3K27me3, a modification predictive of gene repression in preimplantation embryos. Histone variant-specific nucleosome retention in sperm is strongly associated with nucleosome turnover in round spermatids. Our data show evolutionary conservation of the basic principles of nucleosome retention in mouse and human sperm, supporting a model of epigenetic inheritance by nucleosomes between generations.

Preferential growth of short aligned, metallic-rich single-walled carbon nanotubes from perpendicular layered double hydroxide film.

PubMed

Zhao, Meng-Qiang; Tian, Gui-Li; Zhang, Qiang; Huang, Jia-Qi; Nie, Jing-Qi; Wei, Fei

2012-04-07

Direct bulk growth of single-walled carbon nanotubes (SWCNTs) with required properties, such as diameter, length, and chirality, is the first step to realize their advanced applications in electrical and optical devices, transparent conductive films, and high-performance field-effect transistors. Preferential growth of short aligned, metallic-rich SWCNTs is a great challenge to the carbon nanotube community. We report the bulk preferential growth of short aligned SWCNTs from perpendicular Mo-containing FeMgAl layered double hydroxide (LDH) film by a facile thermal chemical vapor deposition with CH(4) as carbon source. The growth of the short aligned SWCNTs showed a decreased growth velocity with an initial value of 1.9 nm s(-1). Such a low growth velocity made it possible to get aligned SWCNTs shorter than 1 μm with a growth duration less than 15 min. Raman spectra with different excitation wavelengths indicated that the as-grown short aligned SWCNTs showed high selectivity of metallic SWCNTs. Various kinds of materials, such as mica, quartz, Cu foil, and carbon fiber, can serve as the substrates for the growth of perpendicular FeMoMgAl LDH films and also the growth of the short aligned SWCNTs subsequently. These findings highlight the easy route for bulk preferential growth of aligned metallic-rich SWCNTs with well defined length for further bulk characterization and applications. This journal is © The Royal Society of Chemistry 2012

Targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae.

PubMed

Takahashi, Tadashi; Sato, Atsushi; Ogawa, Masahiro; Hanya, Yoshiki; Oguma, Tetsuya

2014-08-01

We describe here the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had a 5'-deleted pyrG upstream of the region targeted for tandem chromosomal duplication and a 3'-deleted pyrG downstream of the target region. Consequently,strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks(DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under nonselective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.

NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes.

PubMed

Duewer, David L; Kline, Margaret C; Redman, Janette W; Butler, John M

2004-12-01

Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.

Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

PubMed Central

Ballantyne, Kaye N; Ralf, Arwin; Aboukhalid, Rachid; Achakzai, Niaz M; Anjos, Maria J; Ayub, Qasim; Balažic, Jože; Ballantyne, Jack; Ballard, David J; Berger, Burkhard; Bobillo, Cecilia; Bouabdellah, Mehdi; Burri, Helen; Capal, Tomas; Caratti, Stefano; Cárdenas, Jorge; Cartault, François; Carvalho, Elizeu F; Carvalho, Monica; Cheng, Baowen; Coble, Michael D; Comas, David; Corach, Daniel; D'Amato, Maria E; Davison, Sean; de Knijff, Peter; De Ungria, Maria Corazon A; Decorte, Ronny; Dobosz, Tadeusz; Dupuy, Berit M; Elmrghni, Samir; Gliwiński, Mateusz; Gomes, Sara C; Grol, Laurens; Haas, Cordula; Hanson, Erin; Henke, Jürgen; Henke, Lotte; Herrera-Rodríguez, Fabiola; Hill, Carolyn R; Holmlund, Gunilla; Honda, Katsuya; Immel, Uta-Dorothee; Inokuchi, Shota; Jobling, Mark A; Kaddura, Mahmoud; Kim, Jong S; Kim, Soon H; Kim, Wook; King, Turi E; Klausriegler, Eva; Kling, Daniel; Kovačević, Lejla; Kovatsi, Leda; Krajewski, Paweł; Kravchenko, Sergey; Larmuseau, Maarten H D; Lee, Eun Young; Lessig, Ruediger; Livshits, Ludmila A; Marjanović, Damir; Minarik, Marek; Mizuno, Natsuko; Moreira, Helena; Morling, Niels; Mukherjee, Meeta; Munier, Patrick; Nagaraju, Javaregowda; Neuhuber, Franz; Nie, Shengjie; Nilasitsataporn, Premlaphat; Nishi, Takeki; Oh, Hye H; Olofsson, Jill; Onofri, Valerio; Palo, Jukka U; Pamjav, Horolma; Parson, Walther; Petlach, Michal; Phillips, Christopher; Ploski, Rafal; Prasad, Samayamantri P R; Primorac, Dragan; Purnomo, Gludhug A; Purps, Josephine; Rangel-Villalobos, Hector; Rębała, Krzysztof; Rerkamnuaychoke, Budsaba; Gonzalez, Danel Rey; Robino, Carlo; Roewer, Lutz; Rosa, Alexandra; Sajantila, Antti; Sala, Andrea; Salvador, Jazelyn M; Sanz, Paula; Schmitt, Cornelia; Sharma, Anil K; Silva, Dayse A; Shin, Kyoung-Jin; Sijen, Titia; Sirker, Miriam; Siváková, Daniela; Škaro, Vedrana; Solano-Matamoros, Carlos; Souto, Luis; Stenzl, Vlastimil; Sudoyo, Herawati; Syndercombe-Court, Denise; Tagliabracci, Adriano; Taylor, Duncan; Tillmar, Andreas; Tsybovsky, Iosif S; Tyler-Smith, Chris; van der Gaag, Kristiaan J; Vanek, Daniel; Völgyi, Antónia; Ward, Denise; Willemse, Patricia; Yap, Eric PH; Yong, Rita YY; Pajnič, Irena Zupanič; Kayser, Manfred

2014-01-01

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. PMID:24917567

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching charge...

Short, intermediate and mesoscopic range order in sulfur-rich binary glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bychkov, E.; Miloshova, M.; Price, D.L.

2008-09-29

Pulsed neutron and high-energy X-ray diffraction, small-angle neutron scattering, Raman spectroscopy and DSC were used to study structural changes on the short, intermediate and mesoscopic range scale for sulfur-rich AsS{sub x} (x {ge} 1.5) and GeS{sub x} (x {ge} 2) glasses. Two structural regions were found in the both systems. (1) Between stoichiometric (As{sub 2}S{sub 3} and GeS{sub 2}) and 'saturated' (AsS{sub 2.2} and GeS{sub 2.7}) compositions, excessive sulfur atoms form sulfur dimers and/or short chains, replacing bridging sulfur in corner-sharing AsS{sub 3/2} and GeS{sub 4/2} units. (2) Above the 'saturated' compositions at [As] < 30.5 at.% and [Ge]

Synthesis of extended polycyclic aromatic hydrocarbons by oxidative tandem spirocyclization and 1,2-aryl migration

NASA Astrophysics Data System (ADS)

Zhang, Xuan; Xu, Zhanqiang; Si, Weili; Oniwa, Kazuaki; Bao, Ming; Yamamoto, Yoshinori; Jin, Tienan

2017-04-01

The extended polycyclic aromatic hydrocarbons (PAHs) have received significant interdisciplinary attention due to their semiconducting applications in diverse organic electronics as well as intriguing structural interests of well-defined graphene segments. Herein, a highly efficient oxidative spirocyclization and 1,2-aryl migration tandem synthetic method for the construction of extended polyaromatic hydrocarbons (PAHs) has been developed. The CuCl-catalyst/PhCO3 tBu or DDQ oxidation system in the presence of trifluoroacetic acid enables the selective single-electron oxidation to take place preferentially at the more electron-rich alkene moiety of o-biphenylyl-substituted methylenefluorenes, giving rise to the subsequent tandem process. A variety of structurally diverse extended PAHs including functionalized dibenzo[g,p]chrysenes, benzo[f]naphtho[1,2-s]picene, hexabenzo[a,c,fg,j,l,op]tetracene, tetrabenzo[a,c,f,m]phenanthro[9,10-k]tetraphene, tetrabenzo[a,c,f,k]phenanthro[9,10-m]tetraphene, tetrabenzo[a,c,f,o]phenanthro[9,10-m]picene and S-type helicene have been readily synthesized.

Determination of short chain chlorinated paraffins in water by stir bar sorptive extraction-thermal desorption-gas chromatography-triple quadrupole tandem mass spectrometry.

PubMed

Tölgyessy, P; Nagyová, S; Sládkovičová, M

2017-04-21

A simple, robust, sensitive and environment friendly method for the determination of short chain chlorinated paraffins (SCCPs) in water using stir bar sorptive extraction (SBSE) coupled to thermal desorption-gas chromatography-triple quadrupole tandem mass spectrometry (TD-GC-QqQ-MS/MS) was developed. SBSE was performed using 100mL of water sample, 20mL of methanol as a modifier, and a commercial sorptive stir bar (with 10mm×0.5mm PDMS layer) during extraction period of 16h. After extraction, the sorptive stir bar was thermally desorbed and online analysed by GC-MS/MS. Method performance was evaluated for MilliQ and surface water spiked samples. For both types of matrices, a linear dynamic range of 0.5-3.0μgL -1 with correlation coefficients >0.999 and relative standard deviations (RSDs) of the relative response factors (RRFs) <12% was established. The limits of quantification (LOQs) of 0.06 and 0.08μgL -1 , and the precision (repeatability) of 6.4 and 7.7% (RSDs) were achieved for MilliQ and surface water, respectively. The method also showed good robustness, recovery and accuracy. The obtained performance characteristics indicate that the method is suitable for screening and monitoring and compliance checking with environmental quality standards (EQS, set by the EU) for SCCPs in surface waters. Copyright © 2017 Elsevier B.V. All rights reserved.

[Association of aggressive behaviors of schizophrenia with short tandem repeats loci].

PubMed

Yang, Chun; Ba, Huajie; Tan, Xingqi; Zhao, Hanqing; Zhang, Shuyou; Yu, Haiying

2017-12-10

To assess the association of short tandem repeats (STRs) loci with aggressive behaviors of schizophrenia. Blood samples from 123 schizophrenic patients with aggressive behaviors and 489 schizophrenic patients without aggressive behaviors were collected. DNA from all samples was amplified with a PowerPlex 21 system and separated by electrophoresis to determine the genotypes and allelic frequencies of 20 STR loci including D3S1368, D1S1656, D6S1043, D13S317, Penta E, D16S639, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, and FGA. All of the 20 STR loci have reached Hardy-Weinberg equilibrium in both groups. A significant difference was found in allelic and genotypic frequencies of loci Penta D between the two groups (alleles: P=0.042; genotypes: P=0.014) but not for the remaining 19 loci (P> 0.05). Univariate analysis also showed a significant difference for allele 10 and genotypes 10-12 of Penta D between the two groups (P=0.0027, P=0.0001), with the OR being 1.81 (95%CI: 1.22-2.67) and 4.33 (95%CI: 1.95-9.59), respectively. Penta D may be associated with aggressive behaviors of schizophrenia. Allele 10 and genotypes 10-12 of Penta D may confer a risk for the disease.

Developmental Validation of Short Tandem Repeat Reagent Kit for Forensic DNA Profiling of Canine Biological Materials

PubMed Central

Dayton, Melody; Koskinen, Mikko T; Tom, Bradley K; Mattila, Anna-Maria; Johnston, Eric; Halverson, Joy; Fantin, Dennis; DeNise, Sue; Budowle, Bruce; Smith, David Glenn; Kanthaswamy, Sree

2009-01-01

Aim To develop a reagent kit that enables multiplex polymerase chain reaction (PCR) amplification of 18 short tandem repeats (STR) and the canine sex-determining Zinc Finger marker. Methods Validation studies to determine the robustness and reliability in forensic DNA typing of this multiplex assay included sensitivity testing, reproducibility studies, intra- and inter-locus color balance studies, annealing temperature and cycle number studies, peak height ratio determination, characterization of artifacts such as stutter percentages and dye blobs, mixture analyses, species-specificity, case type samples analyses and population studies. Results The kit robustly amplified domesticated dog samples and consistently generated full 19-locus profiles from as little as 125 pg of dog DNA. In addition, wolf DNA samples could be analyzed with the kit. Conclusion The kit, which produces robust, reliable, and reproducible results, will be made available for the forensic research community after modifications based on this study’s evaluation to comply with the quality standards expected for forensic casework. PMID:19480022

The association of 22 Y chromosome short tandem repeat loci with initiative-aggressive behavior.

PubMed

Yang, Chun; Ba, Huajie; Zhang, Wei; Zhang, Shuyou; Zhao, Hanqing; Yu, Haiying; Gao, Zhiqin; Wang, Binbin

2018-05-15

Aggressive behavior represents an important public concern and a clinical challenge to behaviorists and psychiatrists. Aggression in humans is known to have an important genetic basis, so to investigate the association of Y chromosome short tandem repeat (Y-STR) loci with initiative-aggressive behavior, we compared allelic and haplotypic distributions of 22 Y-STRs in a group of Chinese males convicted of premeditated extremely violent crimes (n = 271) with a normal control group (n = 492). Allelic distributions of DYS533 and DYS437 loci differed significantly between the two groups (P < 0.05). The case group had higher frequencies of DYS533 allele 14, DYS437 allele 14, and haplotypes 11-14 of DYS533-DYS437 compared with the control group. Additionally, the DYS437 allele 15 frequency was significantly lower in cases than controls. No frequency differences were observed in the other 20 Y-STR loci between these two groups. Our results indicate a genetic role for Y-STR loci in the development of initiative aggression in non-psychiatric subjects. Copyright © 2018 Elsevier B.V. All rights reserved.

SMART Digest™ compared with pellet digestion for analysis of human immunoglobulin G1 in rat serum by liquid chromatography tandem mass spectrometry.

PubMed

Lanshoeft, Christian; Heudi, Olivier; Cianférani, Sarah

2016-05-15

The newly developed SMART Digest™ kit was applied for the sample preparation of human immunoglobulin G1 (hIgG1) in rat serum prior to qualitative and quantitative analyses by liquid chromatography tandem mass spectrometry (LC-MS/MS). The sequence coverages obtained for the light and heavy chains of hIgG1A were 50 and 76%, respectively. The calibration curve was linear from 1.00 to 1000 μg/ml for three of four generic peptides. Overall, the SMART Digest™ kit resulted in similar quantitative data (linearity, sensitivity, accuracy, and precision) compared with the pellet digestion protocol. However, the SMART Digest™ required only 2 h of sample preparation with fewer reagents. Copyright © 2016 Elsevier Inc. All rights reserved.

Towards maximizing the haze effect of electrodes for high efficiency hybrid tandem solar cell

NASA Astrophysics Data System (ADS)

Vincent, Premkumar; Song, Dong-Seok; Kwon, Hyeok Bin; Kim, Do-Kyung; Jung, Ji-Hoon; Kwon, Jin-Hyuk; Choe, Eunji; Kim, Young-Rae; Kim, Hyeok; Bae, Jin-Hyuk

2018-02-01

In this study, we executed optical simulations to compute the optimum power conversion efficiency (PCE) of a-Si:H/organic photovoltaic (OPV) hybrid tandem solar cell. The maximum ideal short circuit current density (Jsc,max) of the tandem solar cell is initially obtained by optimizing the thickness of the active layer of the OPV subcell for varying thickness of the a-Si:H bottom subcell. To investigate the effect of Haze parameter on the ideal short-circuit current density (Jsc,ideal) of the solar cells, we have varied the haze ratio for the TCO electrode of the a-Si:H subcell in the tandem structure. The haze ratio was obtained for various root mean square (RMS) roughness of the TCO of the front cell. The effect of haze ratio on the Jsc,ideal on the tandem structured solar cell was studied, and the highest Jsc,ideal was obtained at a haze of 55.5% when the thickness of the OPV subcell was 150 nm and that of the a-Si:H subcell was 500 nm.

A Comparison of Tandem Walk Performance Between Bed Rest Subjects and Astronauts

NASA Technical Reports Server (NTRS)

Miller, Chris; Peters, Brian; Kofman, Igor; Philips, Tiffany; Batson, Crystal; Cerisano, Jody; Fisher, Elizabeth; Mulavara, Ajitkumar; Feiveson, Alan; Reschke, Millard;

Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

PubMed

Fungtammasan, Arkarachai; Tomaszkiewicz, Marta; Campos-Sánchez, Rebeca; Eckert, Kristin A; DeGiorgio, Michael; Makova, Kateryna D

2016-10-01

Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA-DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated transcript sequence variation for short tandem repeats (STRs). We developed the first maximum-likelihood estimator (MLE) to infer RT error and RDD rates, taking next generation sequencing error rates into account. Using the MLE, we empirically evaluated RT error and RDD rates for STRs in a large-scale DNA and RNA replicated sequencing experiment conducted in a primate species. The RT error rates increased exponentially with STR length and were biased toward expansions. The RDD rates were approximately 1 order of magnitude lower than the RT error rates. The RT error rates estimated with the MLE from a primate data set were concordant with those estimated with an independent method, barcoded RNA sequencing, from a Caenorhabditis elegans data set. Our results have important implications for medical genomics, as STR allelic variation is associated with >40 diseases. STR nonallelic transcript variation can also contribute to disease phenotype. The MLE and empirical rates presented here can be used to evaluate the probability of disease-associated transcripts arising due to RDD. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Basic Fibroblast Growth Factor Fused with Tandem Collagen-Binding Domains from Clostridium histolyticum Collagenase ColG Increases Bone Formation.

PubMed

Sekiguchi, Hiroyuki; Uchida, Kentaro; Matsushita, Osamu; Inoue, Gen; Nishi, Nozomu; Masuda, Ryo; Hamamoto, Nana; Koide, Takaki; Shoji, Shintaro; Takaso, Masashi

2018-01-01

Basic fibroblast growth factor 2 (bFGF) accelerates bone formation during fracture healing. Because the efficacy of bFGF decreases rapidly following its diffusion from fracture sites, however, repeated dosing is required to ensure a sustained therapeutic effect. We previously developed a fusion protein comprising bFGF, a polycystic kidney disease domain (PKD; s2b), and collagen-binding domain (CBD; s3) sourced from the Clostridium histolyticum class II collagenase, ColH, and reported that the combination of this fusion protein with a collagen-like peptide, poly(Pro-Hyp-Gly) 10 , induced mesenchymal cell proliferation and callus formation at fracture sites. In addition, C. histolyticum produces class I collagenase (ColG) with tandem CBDs (s3a and s3b) at the C-terminus. We therefore hypothesized that a bFGF fusion protein containing ColG-derived tandem CBDs (s3a and s3b) would show enhanced collagen-binding activity, leading to improved bone formation. Here, we examined the binding affinity of four collagen anchors derived from the two clostridial collagenases to H-Gly-Pro-Arg-Gly-(Pro-Hyp-Gly) 12 -NH 2 , a collagenous peptide, by surface plasmon resonance and found that tandem CBDs (s3a-s3b) have the highest affinity for the collagenous peptide. We also constructed four fusion proteins consisting of bFGF and s3 (bFGF-s3), s2b-s3b (bFGF-s2b-s3), s3b (bFGF-s3b), and s3a-s3b (bFGF-s3a-s3b) and compared their biological activities to those of a previous fusion construct (bFGF-s2b-s3) using a cell proliferation assay in vitro and a mouse femoral fracture model in vivo. Among these CB-bFGFs, bFGF-s3a-s3b showed the highest capacity to induce mesenchymal cell proliferation and callus formation in the mice fracture model. The poly(Pro-Hyp-Gly) 10 /bFGF-s3a-s3b construct may therefore have the potential to promote bone formation in clinical settings.

Mutation rates at 42 Y chromosomal short tandem repeats in Chinese Han population in Eastern China.

PubMed

Wu, Weiwei; Ren, Wenyan; Hao, Honglei; Nan, Hailun; He, Xin; Liu, Qiuling; Lu, Dejian

2018-01-31

Mutation analysis of 42 Y chromosomal short tandem repeats (Y-STRs) loci was performed using a sample of 1160 father-son pairs from the Chinese Han population in Eastern China. The results showed that the average mutation rate across the 42 Y-STR loci was 0.0041 (95% CI 0.0036-0.0047) per locus per generation. The locus-specific mutation rates varied from 0.000 to 0.0190. No mutation was found at DYS388, DYS437, DYS448, DYS531, and GATA_H4. DYS627, DYS570, DYS576, and DYS449 could be classified as rapidly mutating Y-STRs, with mutation rates higher than 1.0 × 10 -2 . DYS458, DYS630, and DYS518 were moderately mutating Y-STRs, with mutation rates ranging from 8 × 10 -3 to 1 × 10 -2 . Although the characteristics of the Y-STR mutations were consistent with those in previous studies, mutation rate differences between our data and previous published data were found at some rapidly mutating Y-STRs. The single-copy loci located on the short arm of the Y chromosome (Yp) showed relatively higher mutation rates more frequently than the multi-copy loci. These results will not only extend the data for Y-STR mutations but also be important for kinship analysis, paternal lineage identification, and family relationship reconstruction in forensic Y-STR analysis.

Proteins in Load-Bearing Junctions: The Histidine-Rich Metal-Binding Protein of Mussel Byssus†,‡

PubMed Central

Zhao, Hua; Waite, J. Herbert

2007-01-01

Building complex load-bearing scaffolds depends on effective ways of joining functionally different biomacromolecules. The junction between collagen fibers and foamlike adhesive plaques in mussel byssus is robust despite the strikingly dissimilar connected structures. mcfp-4, the matrix protein from this junction, and its presecreted form from the foot tissue of Mytilus californianus were isolated and characterized. mcfp-4 has a mass of ∼93 kDa as determined by MALDI-TOF mass spectrometry. Its composition is dominated by histidine (22 mol %), but levels of lysine, arginine, and aspartate are also significant. A small amount of 3,4-dihydroxyphenyl-L-alanine (2 mol %) can be detected by amino acid analysis and redox cycling assays. The cDNA-deduced sequence of mcfp-4 reveals multiple variants with highly repetitive internal structures, including ∼36 tandemly repeated His-rich decapeptides (e.g., HVHTHRVLHK) in the N-terminal half and 16 somewhat more degenerate aspartate-rich undecapeptides (e.g., DDHVNDIAQTA) in the C-terminal half. Incubation of a synthetic peptide based on the His-rich decapeptide with Fe3+, Co2+, Ni2+, Zn2+, and Cu2+ indicates that only Cu is strongly bound. MALDI-TOF mass spectrometry of the peptide modified with diethyl pyrocarbonate before and after Cu binding suggests that histidine residues dominate Cu binding. In contrast, the aspartate-rich undecapeptides preferentially bind Ca2+. mcfp-4 is strategically positioned to function as a macromolecular bifunctional linker by using metal ions to couple its own His-rich domains to the His-rich termini of the preCOLs. Ca2+ may mediate coupling of the C-terminus to other calcium-binding plaque proteins. PMID:17115717

MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.

PubMed

Pratt, Brian; Howbert, J Jeffry; Tasman, Natalie I; Nilsson, Erik J

2012-01-01

MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. brian.pratt@insilicos.com

Short tandem repeat DNA typing provides an international reference standard for authentication of human cell lines.

PubMed

Dirks, Wilhelm Gerhard; Faehnrich, Silke; Estella, Isabelle Annick Janine; Drexler, Hans Guenter

2005-01-01

Cell lines have wide applications as model systems in the medical and pharmaceutical industry. Much drug and chemical testing is now first carried out exhaustively on in vitro systems, reducing the need for complicated and invasive animal experiments. The basis for any research, development or production program involving cell lines is the choice of an authentic cell line. Microsatellites in the human genome that harbour short tandem repeat (STR) DNA markers allow individualisation of established cell lines at the DNA level. Fluorescence polymerase chain reaction amplification of eight highly polymorphic microsatellite STR loci plus gender determination was found to be the best tool to screen the uniqueness of DNA profiles in a fingerprint database. Our results demonstrate that cross-contamination and misidentification remain chronic problems in the use of human continuous cell lines. The combination of rapidly generated DNA types based on single-locus STR and their authentication or individualisation by screening the fingerprint database constitutes a highly reliable and robust method for the identification and verification of cell lines.

MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services

PubMed Central

Pratt, Brian; Howbert, J. Jeffry; Tasman, Natalie I.; Nilsson, Erik J.

2012-01-01

Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. Contact: brian.pratt@insilicos.com PMID:22072385

Enhanced fill factor of tandem organic solar cells incorporating a diketopyrrolopyrrole-based low-bandgap polymer and optimized interlayer.

PubMed

Wang, Dong Hwan; Kyaw, Aung Ko Ko; Park, Jong Hyeok

2015-01-01

We demonstrate that reproducible results can be obtained from tandem solar cells based on the wide-bandgap poly[N-9'-heptadecanyl-2,7-carbazole-alt-5,5-(4,7-di-2-thienyl-2',1',3'-benzothiadiazole] (PCDTBT) and the diketopyrrolopyrrole (DPP)-based narrow bandgap polymer (DT-PDPP2T-TT) with a decyltetradecyl (DT) and an electron-rich 2,5-di-2-thienylthieno[3,2-b]thiophene (2T-TT) group fabricated using an optimized interlayer (ZnO NPs/ph-n-PEDOT:PSS) [NPs: nanoparticles; ph-n: pH-neutral PEDOT: poly(3,4-ethylenedioxythiophene); PSS: polystyrene sulfonate]. The tandem cells are fabricated by applying a simple process without thermal annealing. The ZnO NP interlayer operates well when the ZnO NPs are dispersed in 2-methoxyethanol, as no precipitation and chemical reactions occur. In addition to the ZnO NP film, we used neutral PEDOT:PSS as a second interlayer which is not affect to the sequential deposited bulk heterojunction (BHJ) active layer of acidification. The power conversion efficiency (PCE) of a tandem device reaches 7.4 % (open-circuit voltage VOC =1.53 V, short-circuit current density JSC =7.3 mA cm(-2) , and fill factor FF=67 %). Furthermore, FF is increased to up to 71 % when another promising large bandgap (bandgap ∼1.94 eV) polymer (PBnDT-FTAZ) is used. The surface of each layer with nanoscale morphology (BHJ1/ZnO NPs film/ph-n-PEDOT:PSS/BHJ2) was examined by means of AFM analysis during sequential processing. The combination of these factors, efficient DPP-based narrow bandgap material and optimized interlayer, leads to the high FF (average approaches 70 %) and reproducibly operating tandem BHJ solar cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The K2-ESPRINT project. VI. K2-105 b, a hot Neptune around a metal-rich G-dwarf

NASA Astrophysics Data System (ADS)

Narita, Norio; Hirano, Teruyuki; Fukui, Akihiko; Hori, Yasunori; Dai, Fei; Yu, Liang; Livingston, John; Ryu, Tsuguru; Nowak, Grzegorz; Kuzuhara, Masayuki; Sato, Bun'ei; Takeda, Yoichi; Albrecht, Simon; Kudo, Tomoyuki; Kusakabe, Nobuhiko; Palle, Enric; Ribas, Ignasi; Tamura, Motohide; Van Eylen, Vincent; Winn, Joshua N.

2017-04-01

We report on the confirmation that the candidate transits observed for the star EPIC 211525389 are due to a short-period Neptune-sized planet. The host star, located in K2 campaign field 5, is a metal-rich ([Fe/H] = 0.26 ± 0.05) G-dwarf (Teff = 5430 ± 70 K and log g = 4.48 ± 0.09), based on observations with the High Dispersion Spectrograph (HDS) on the Subaru 8.2 m telescope. High spatial resolution AO imaging with HiCIAO on the Subaru telescope excludes faint companions near the host star, and the false positive probability of this target is found to be <10-6 using the open source vespa code. A joint analysis of transit light curves from K2 and additional ground-based multi-color transit photometry with MuSCAT on the Okayama 1.88 m telescope gives an orbital period of P = 8.266902 ± 0.000070 d and consistent transit depths of Rp/R⋆ ∼ 0.035 or (Rp/R⋆)2 ∼ 0.0012. The transit depth corresponds to a planetary radius of R_p = 3.59_{-0.39}^{+0.44} R_{\\oplus }, indicating that EPIC 211525389 b is a short-period Neptune-sized planet. Radial velocities of the host star, obtained with the Subaru HDS, lead to a 3 σ upper limit of 90 M⊕ (0.00027 M⊙) on the mass of EPIC 211525389 b, confirming its planetary nature. We expect this planet, newly named K2-105 b, to be the subject of future studies to characterize its mass, atmosphere, and spin-orbit (mis)alignment, as well as investigate the possibility of additional planets in the system.

Filipino DNA variation at 12 X-chromosome short tandem repeat markers.

PubMed

Salvador, Jazelyn M; Apaga, Dame Loveliness T; Delfin, Frederick C; Calacal, Gayvelline C; Dennis, Sheila Estacio; De Ungria, Maria Corazon A

2018-06-08

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator ® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq ™ DNA Signature Prep kit of the MiSeq ® FGx ™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications. Copyright © 2018 Elsevier B.V. All rights reserved.

THE SUPER LITHIUM-RICH RED GIANT RAPID ROTATOR G0928+73.2600: A CASE FOR PLANET ACCRETION?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlberg, Joleen K.; Majewski, Steven R.; Rood, Robert T.

2010-11-01

We present the discovery of a super lithium-rich K giant star, G0928+73.2600. This red giant (T {sub eff} = 4885 K and log g = 2.65) is a fast rotator with a projected rotational velocity of 8.4 km s{sup -1} and an unusually high lithium abundance of A(Li) = 3.30 dex. Although the lack of a measured parallax precludes knowing the exact evolutionary phase, an isochrone-derived estimate of its luminosity places the star on the Hertzsprung-Russell diagram in a location that is not consistent with either the red bump on the first ascent of the red giant branch or withmore » the second ascent on the asymptotic giant branch, the two evolutionary stages where lithium-rich giant stars tend to cluster. Thus, even among the already unusual group of lithium-rich giant stars, G0928+73.2600 is peculiar. Using {sup 12}C/{sup 13}C as a tracer for mixing-more mixing leads to lower {sup 12}C/{sup 13}C-we find {sup 12}C/{sup 13}C = 28, which is near the expected value for standard first dredge-up mixing. We can therefore conclude that 'extra' deep mixing has not occurred. Regardless of the ambiguity of the evolutionary stage, the extremely large lithium abundance and the rotational velocity of this star are unusual, and we speculate that G0928+73.2600 has been enriched in both lithium and angular momentum from a sub-stellar companion.« less

Improved efficiency of perovskite-silicon tandem solar cell near the matched optical absorption between the subcells

NASA Astrophysics Data System (ADS)

Iftiquar, S. M.; Jung, Junhee; Yi, Junsin

2017-10-01

Current matching in a tandem solar cell is significant, because in a mismatched device the lowest current generating subcell becomes the current limiting component, and overall device efficiency remains lower than that could be obtained in the current matched device. Recent reports on methyl ammonium lead iodide (MAPbI3) based thin film solar cell has drawn interest to a perovskite-silicon tandem solar cell. Therefore, we investigated such a tandem solar cell theoretically. We used a MAPbI3 based top and heterojunction with intrinsic thin layer silicon (HIT) bottom subcell. Optimization of the device structure was carried out by varying thickness of perovskite layer of top-cell from 50 to 1000 nm, while thickness of active layer of the HIT cell was kept constant, to 500 µm. Single-junction solar cell, formed with the bottom subcell had open circuit voltage (V oc) of 705.1 mV, short circuit current density (J sc) of 28.22 mA cm-2, fill factor (FF) of 0.82 and efficiency of 16.4% under AM1.5G insolation. A relatively low thickness (150 nm) of the perovskite absorber layer was found optimum for the top-subcell to achieve best efficiency of the tandem cell, partly because of intermediate reflection at the interface between the two cells. We obtained a maximum of 20.92% efficiency of the tandem solar cell, which is higher by a factor of 1.27 from the starting HIT cell and a factor 1.47 higher from the perovskite cell efficiency. J sc of the optimized tandem cell was 13.06 mA cm-2. This was achieved near the matching optical absorption or current-density of the component subcells. For a practical application, the device used in our investigation was without textured front surface. An ordinary HIT bottom-cell was used with lower J sc. Therefore, with an improved HIT subcell, efficiency of the tandem cell, higher than 21% will be achievable.

Integration of E. coli aroG-pheA tandem genes into Corynebacterium glutamicum tyrA locus and its effect on L-phenylalanine biosynthesis

PubMed Central

Liu, Dong-Xin; Fan, Chang-Sheng; Tao, Ju-Hong; Liang, Guo-Xin; Gao, Shan-E; Wang, Hai-Jiao; Li, Xin; Song, Da-Xin

2004-01-01

AIM: To study the effect of integration of tandem aroG-pheA genes into the tyrA locus of Corynebacterium glutamicum (C. glutamicum) on the production of L-phenylalanine. METHODS: By nitrosoguanidine mutagenesis, five p-fluorophenylalanine (FP)-resistant mutants of C.glutamicum FP were selected. The tyrA gene encoding prephenate dehydrogenase (PDH) of C.glutamicum was amplified by polymerase chain reaction (PCR) and cloned on the plasmid pPR. Kanamycin resistance gene (Km) and the PBF-aroG-pheA-T (GA) fragment of pGA were inserted into tyrA gene to form targeting vectors pTK and pTGAK, respectively. Then, they were transformed into C.glutamicum FP respectively by electroporation. Cultures were screened by a medium containing kanamycin and detected by PCR and phenotype analysis. The transformed strains were used for L-phenylalanine fermentation and enzyme assays. RESULTS: Engineering strains of C.glutamicum (Tyr-) were obtained. Compared with the original strain, the transformed strain C. glutamicum GAK was observed to have the highest elevation of L-phenylalanine production by a 1.71-fold, and 2.9-, 3.36-, and 3.0-fold in enzyme activities of chorismate mutase, prephenate dehydratase and 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase, respectively. CONCLUSION: Integration of tandem aroG-pheA genes into tyrA locus of C. glutamicum chromosome can disrupt tyrA gene and increase the yield of L-phenylalanine production. PMID:15534933

Versatile communication strategies among tandem WW domain repeats

PubMed Central

Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar

2015-01-01

Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands. PMID:25710931

Hog Charm II tetracycline test screening results compared with a liquid chromatography tandem mass spectrometry 10-μg/kg method.

PubMed

Salter, Robert; Holmes, Steven; Legg, David; Coble, Joel; George, Bruce

2012-02-01

Pork tissue samples that tested positive and negative by the Charm II tetracycline test screening method in the slaughter plant laboratory were tested with the modified AOAC International liquid chromatography tandem mass spectrometry (LC-MS-MS) method 995.09 to determine the predictive value of the screening method at detecting total tetracyclines at 10 μg/kg of tissue, in compliance with Russian import regulations. There were 218 presumptive-positive tetracycline samples of 4,195 randomly tested hogs. Of these screening test positive samples, 83% (182) were positive, >10 μg/kg by LC-MS-MS; 12.8% (28) were false violative, greater than limit of detection (LOD) but <10 μg/kg; and 4.2% (8) were not detected at the LC-MS-MS LOD. The 36 false-violative and not-detected samples represent 1% of the total samples screened. Twenty-seven of 30 randomly selected tetracycline screening negative samples tested below the LC-MS-MS LOD, and 3 samples tested <3 μg/kg chlortetracycline. Results indicate that the Charm II tetracycline test is effective at predicting hogs containing >10 μg/kg total tetracyclines in compliance with Russian import regulations.

Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

PubMed Central

Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

1997-01-01

RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

Multivalent binding of formin-binding protein 21 (FBP21)-tandem-WW domains fosters protein recognition in the pre-spliceosome.

PubMed

Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

2011-11-04

The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome.

Allele Frequencies for 15 Short Tandem Repeat Loci in Representative Sample of Croatian Population

PubMed Central

Projić, Petar; Škaro, Vedrana; Šamija, Ivana; Pojskić, Naris; Durmić-Pašić, Adaleta; Kovačević, Lejla; Bakal, Narcisa; Primorac, Dragan; Marjanović, Damir

2007-01-01

Aim To study the distribution of allele frequencies of 15 short tandem repeat (STR) loci in a representative sample of the Croatian population. Methods A total of 195 unrelated Caucasian individuals born in Croatia, from 14 counties and the City of Zagreb, were sampled for the analysis. All the tested individuals were voluntary donors. Buccal swab was used as the DNA source. AmpFlSTR® Identifiler® was applied to simultaneously amplify 15 STR loci. Total reaction volume was 12.5 μL. The polymerase chain reaction (PCR) amplification was carried out in PE Gene Amp PCR System Thermal Cycler. Electrophoresis of the amplification products was preformed on an ABI PRISM 3130 Genetic Analyzer. After PCR amplification and separation by electrophoresis, raw data were compiled, analyzed, and numerical allele designations of the profiles were obtained. Deviation from Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, and power of exclusion were calculated. Bonferroni’s correction was used before each comparative analysis. Results We compared Croatian data with those obtained from geographically neighboring European populations. The significant difference (at P<0.01) in allele frequencies was recorded only between the Croatian and Slovenian populations for vWA locus. There was no significant deviation from Hardy-Weinberg equilibrium for all the observed loci. Conclusion Obtained population data concurred with the expected “STR data frame” for this part of Europe. PMID:17696301

Strong transcription blockage mediated by R-loop formation within a G-rich homopurine–homopyrimidine sequence localized in the vicinity of the promoter

PubMed Central

Soo Shin, Jane Hae

2017-01-01

Abstract Guanine-rich (G-rich) homopurine–homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA–DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA–DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription ‘bursting’) and may also have practical implications for the design of expression vectors. PMID:28498974

Substructure of a Tunisian Berber population as inferred from 15 autosomal short tandem repeat loci.

PubMed

Khodjet-El-Khil, Houssein; Fadhlaoui-Zid, Karima; Gusmão, Leonor; Alves, Cíntia; Benammar-Elgaaied, Amel; Amorim, Antonio

2008-08-01

Currently, language and cultural practices are the only criteria to distinguish between Berber autochthonous Tunisian populations. To evaluate these populations' possible genetic structure and differentiation, we have analyzed 15 autosomal short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, and D19S433) in three southern Tunisian Berber groups: Sened, Matmata, and Chenini-Douiret. The exact test of population differentiation based on allele frequencies at the 15 loci shows significant P values at 7 loci between Chenini-Douiret and both Sened and Matmata, whereas just 5 loci show significant P values between Sened and Matmata. Comparative analyses between the three Berber groups based on genetic distances show that P values for F(ST) distances are significant between the three Berber groups. Population analysis performed using Structure shows a clear differentiation between these Berber groups, with strong genetic isolation of Chenini-Douiret. These results confirm at the autosomal level the high degree of heterogeneity of Tunisian Berber populations that had been previously reported for uniparental markers.

Serum Stabilities of Short Tryptophan- and Arginine-Rich Antimicrobial Peptide Analogs

PubMed Central

Nguyen, Leonard T.; Chau, Johnny K.; Perry, Nicole A.; de Boer, Leonie; Zaat, Sebastian A. J.; Vogel, Hans J.

2010-01-01

Background Several short antimicrobial peptides that are rich in tryptophan and arginine residues were designed with a series of simple modifications such as end capping and cyclization. The two sets of hexapeptides are based on the Trp- and Arg-rich primary sequences from the “antimicrobial centre” of bovine lactoferricin as well as an antimicrobial sequence obtained through the screening of a hexapeptide combinatorial library. Methodology/Principal Findings HPLC, mass spectrometry and antimicrobial assays were carried out to explore the consequences of the modifications on the serum stability and microbicidal activity of the peptides. The results show that C-terminal amidation increases the antimicrobial activity but that it makes little difference to its proteolytic degradation in human serum. On the other hand, N-terminal acetylation decreases the peptide activities but significantly increases their protease resistance. Peptide cyclization of the hexameric peptides was found to be highly effective for both serum stability and antimicrobial activity. However the two cyclization strategies employed have different effects, with disulfide cyclization resulting in more active peptides while backbone cyclization results in more proteolytically stable peptides. However, the benefit of backbone cyclization did not extend to longer 11-mer peptides derived from the same region of lactoferricin. Mass spectrometry data support the serum stability assay results and allowed us to determine preferred proteolysis sites in the peptides. Furthermore, isothermal titration calorimetry experiments showed that the peptides all had weak interactions with albumin, the most abundant protein in human serum. Conclusions/Significance Taken together, the results provide insight into the behavior of the peptides in human serum and will therefore aid in advancing antimicrobial peptide design towards systemic applications. PMID:20844765

Tandem Solar Cells from Solution-Processed CdTe and PbS Quantum Dots Using a ZnTe-ZnO Tunnel Junction.

PubMed

Crisp, Ryan W; Pach, Gregory F; Kurley, J Matthew; France, Ryan M; Reese, Matthew O; Nanayakkara, Sanjini U; MacLeod, Bradley A; Talapin, Dmitri V; Beard, Matthew C; Luther, Joseph M

2017-02-08

We developed a monolithic CdTe-PbS tandem solar cell architecture in which both the CdTe and PbS absorber layers are solution-processed from nanocrystal inks. Due to their tunable nature, PbS quantum dots (QDs), with a controllable band gap between 0.4 and ∼1.6 eV, are a promising candidate for a bottom absorber layer in tandem photovoltaics. In the detailed balance limit, the ideal configuration of a CdTe (E g = 1.5 eV)-PbS tandem structure assumes infinite thickness of the absorber layers and requires the PbS band gap to be 0.75 eV to theoretically achieve a power conversion efficiency (PCE) of 45%. However, modeling shows that by allowing the thickness of the CdTe layer to vary, a tandem with efficiency over 40% is achievable using bottom cell band gaps ranging from 0.68 and 1.16 eV. In a first step toward developing this technology, we explore CdTe-PbS tandem devices by developing a ZnTe-ZnO tunnel junction, which appropriately combines the two subcells in series. We examine the basic characteristics of the solar cells as a function of layer thickness and bottom-cell band gap and demonstrate open-circuit voltages in excess of 1.1 V with matched short circuit current density of 10 mA/cm 2 in prototype devices.

Tandem Solar Cells from Solution-Processed CdTe and PbS Quantum Dots Using a ZnTe–ZnO Tunnel Junction

DOE PAGES

Crisp, Ryan W.; Pach, Gregory F.; Kurley, J. Matthew; ...

2017-01-10

Here, we developed a monolithic CdTe-PbS tandem solar cell architecture in which both the CdTe and PbS absorber layers are solution-processed from nanocrystal inks. Due to their tunable nature, PbS quantum dots (QDs), with a controllable band gap between 0.4 and ~1.6 eV, are a promising candidate for a bottom absorber layer in tandem photovoltaics. In the detailed balance limit, the ideal configuration of a CdTe (E g = 1.5 eV)-PbS tandem structure assumes infinite thickness of the absorber layers and requires the PbS band gap to be 0.75 eV to theoretically achieve a power conversion efficiency (PCE) of 45%.more » But, modeling shows that by allowing the thickness of the CdTe layer to vary, a tandem with efficiency over 40% is achievable using bottom cell band gaps ranging from 0.68 and 1.16 eV. In a first step toward developing this technology, we explore CdTe-PbS tandem devices by developing a ZnTe-ZnO tunnel junction, which appropriately combines the two subcells in series. Furthermore, we examine the basic characteristics of the solar cells as a function of layer thickness and bottom-cell band gap and demonstrate open-circuit voltages in excess of 1.1 V with matched short circuit current density of 10 mA/cm 2 in prototype devices.« less

The Alto Tandem and Isol Facility at IPN Orsay

NASA Astrophysics Data System (ADS)

Franchoo, Serge

Alto is an infrastructure for experimental nuclear physics in France that comprises both an on-line isotope-separation facility based on the photofission of uranium and a stable-ion beam facility based on a 14.5-MV tandem accelerator. The isotope-separation on-line section of Alto is dedicated to the production of neutron-rich radioactive ion beams (RIB) from the interaction of the γ-flux induced by a 50-MeV 10-µA electron beam in a uranium-carbide target. It is dimensioned for 1011 fissions per second. The RIB facility is exploited in alternating mode with the tandem-based section of Alto, capable of accelerating both light ions for nuclear astrophysics and heavy ions for γ-spectroscopy. The facility thereby offers the opportunity to deliver beams to a large range of physics programmes from nuclear to interdisciplinary physics. In this article, we present the Alto facility as well as some of the highlights and prospects of the experimental programme.

Rare Sequence Variation in the Genome Flanking a Short Tandem Repeat Locus Can Lead to a Question of “Nonmaternity”

PubMed Central

Deucher, Anne; Chiang, Tsoyu; Schrijver, Iris

2010-01-01

Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed. PMID:20203001

Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter.

PubMed

Belotserkovskii, Boris P; Soo Shin, Jane Hae; Hanawalt, Philip C

2017-06-20

Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA-DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA-DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription 'bursting') and may also have practical implications for the design of expression vectors. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multivalent Binding of Formin-binding Protein 21 (FBP21)-Tandem-WW Domains Fosters Protein Recognition in the Pre-spliceosome*

PubMed Central

Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

2011-01-01

The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome. PMID:21917930

Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.

PubMed

Guédin, Aurore; Lin, Linda Yingqi; Armane, Samir; Lacroix, Laurent; Mergny, Jean-Louis; Thore, Stéphane; Yatsunyk, Liliya A

2018-06-01

Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.

Hierarchical modeling of genome-wide Short Tandem Repeat (STR) markers infers native American prehistory.

PubMed

Lewis, Cecil M

2010-02-01

This study examines a genome-wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan-Paezan and Equatorial-Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan-Paezan populations in Central America emerge together at the tips of the Chibchan-Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan-Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial-Tucanoan and Ge-Pano-Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America. 2009 Wiley-Liss, Inc.

Analysis of short tandem repeat polymorphisms using infrared fluorescence with M18 tailed primers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oetting, W.S.; Wiesner, G.; Laken, S.

The use of short tandem repeat polymorphisms (STRPs) are becoming increasingly important as markers for linkage analysis due to their large numbers of the human genome and their high degree of polymorphism. Fluorescence based detection of the STRP pattern using the LI-COR model 4000S automated DNA sequencer eliminates the need for radioactivity and produces a digitized image that can be used for the analysis of the polymorphisms. In an effort to reduce the cost of STRP analysis, we have synthesized primers with a 19 bp extension complementary to the sequence of the M13 primer on the 5{prime} end of onemore » of the two primers used in the amplification of the STRP instead of using primers with direct conjugation of the infrared fluorescent dye. Up to 5 primer pairs can be multiplexed together with the M13 primer-dye conjugate as the sole primer conjugated to the fluorescent dye. Comparisons between primers that have been directly conjugated to the fluor with those having the M13 sequence extension show no difference in the ability to determine the STRP pattern. At present, the entire Weber 4A set of STRP markers is available with the M13 5{prime} extension. We are currently using this technique for linkage analysis of familial breast cancer and asthma. The combination of STRP analysis using fluorescence detection will allow this technique to be fully automated for allele scoring and linkage analysis.« less

Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases

PubMed Central

Rogers, Faye A; Lloyd, Janice A; Tiwari, Meetu Kaushik

2014-01-01

Triplex structures generated by sequence-specific triplex-forming oligonucleotides (TFOs) have proven to be promising tools for gene targeting strategies. In addition, triplex technology has been highly utilized to study the molecular mechanisms of DNA repair, recombination and mutagenesis. However, triplex formation utilizing guanine-rich oligonucleotides as third strands can be inhibited by potassium-induced self-association resulting in G-quadruplex formation. We report here that guanine-rich TFOs partially substituted with 8-aza-7-deaza-guanine (PPG) have improved target site binding in potassium compared with TFOs containing the natural guanine base. We designed PPG-substituted TFOs to bind to a polypurine sequence in the supFG1 reporter gene. The binding efficiency of PPG-substituted TFOs to the target sequence was analyzed using electrophoresis mobility gel shift assays. We have determined that in the presence of potassium, the non-substituted TFO, AG30 did not bind to its target sequence, however binding was observed with the PPG-substituted AG30 under conditions with up to 140 mM KCl. The PPG-TFOs were able to maintain their ability to induce genomic modifications as measured by an assay for gene-targeted mutagenesis. In addition, these compounds were capable of triplex-induced DNA double strand breaks, which resulted in activation of apoptosis. PMID:25483840

A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

PubMed Central

Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

2011-01-01

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt.

PubMed

Alfonse, Lauren E; Garrett, Amanda D; Lun, Desmond S; Duffy, Ken R; Grgicak, Catherine M

2018-01-01

DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA. The data, generated under 144 laboratory conditions, are classified by total copy number and contributor proportions. For the 70% of samples that were synthetically compromised, we report the level of DNA damage using quantitative and end-point PCR. In addition, we characterize the complexity of the signal by exploring the number of detected alleles in each profile. Copyright © 2017 Elsevier B.V. All rights reserved.

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database.

PubMed

Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

2011-07-01

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers.

PubMed

Asari, Masaru; Okuda, Katsuhiro; Hoshina, Chisato; Omura, Tomohiro; Tasaki, Yoshikazu; Shiono, Hiroshi; Matsubara, Kazuo; Shimizu, Keiko

2016-02-01

The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

The Cold Dust Content of the Oxygen-rich Supernova Remnant G292.0+1.8

NASA Astrophysics Data System (ADS)

Ghavamian, Parviz; Williams, Brian J.

2016-11-01

We present far-infrared images of the Galactic oxygen-rich supernova remnant (SNR) G292.0+1.8, acquired with the PACS and SPIRE instruments of the Herschel Space Observatory. We find that the SNR shell is detected in the PACS blue (100 μm) band, but not in the red (160 μm) band, broadly consistent with results from AKARI observations. There is no discernible emission from G292.0+1.8 in SPIRE imagery at 250, 350 and 500 μm. Comparing the 100 μm emission to that observed with Spitzer at 24 and 70 μm, we find a very similar appearance for G292.0+1.8 at all three wavelengths. The infrared emission is dominated by dust from non-radiative circumstellar shocks. In addition, the radiatively shocked O-rich clump known as the “Spur” on the eastern side of G292.0+1.8 is clearly detected in the PACS blue images, with marginal detection in the red. Fitting the existing 14-40 μm IRS spectra of the Spur together with photometric measurements from 70 μm MIPS and 100 μm PACS photometry, we place an upper limit of ≲ 0.04 M ⊙ of ejecta dust mass in the Spur, under the most conservative assumption that the ejecta dust has a temperature of 15 K. Modeling the dust continuum in the IRS spectra at four positions around the rim, we estimate post-shock densities ranging from {n}p=3.5 cm-3 to 11 cm-3. The integrated spectrum of the entire SNR, dominated by swept-up circumstellar dust, can be fitted with a two-component dust model with a silicate component at 62 K and graphite component at 40 K for a total dust mass of 0.023 M ⊙.

Highly efficient nuclear DNA typing of the World War II skeletal remains using three new autosomal short tandem repeat amplification kits with the extended European Standard Set of loci

PubMed Central

Zupanič Pajnič, Irena; Gornjak Pogorelc, Barbara; Balažic, Jože; Zupanc, Tomaž; Štefanič, Borut

2012-01-01

Aim To perform an efficiency study of three new amplification kits with the extended European Standard Set (ESS) of loci for autosomal short tandem repeat (STR) typing of skeletal remains excavated from the World War II mass graves in Slovenia. Methods In the beginning of the 2011, we analyzed 102 bones and teeth using the PowerPlex ESX 17 System (Promega), AmpFiSTR NGM PCR Amplification Kit (Applied Biosystems), and Investigator ESSplex Kit (Qiagen). We cleaned the bones and teeth, removed surface contamination, and ground them into a powder using liquid nitrogen. Prior to DNA isolation with Biorobot EZ1 (Qiagen), 0.5 g bone or tooth powder was decalcified. Nuclear DNA of the samples was quantified using real-time polymerase chain reaction. All three kits used the same extract with the amplification conditions recommended by the manufacturers. Results We extracted up to 131 ng DNA/g of powder from the bones and teeth. All three amplification kits showed very similar efficiency, since DNA typing was successful with all amplification kits in 101 out of 102 bones and teeth, which represents a 99% success rate. Conclusion The commercially available ESX 17, ESSplex, and NGM kits are highly reliable for STR typing of World War II skeletal remains with the DNA extraction method optimized in our laboratory. PMID:22351574

Effects of supplementation with a calcium-rich marine-derived multi-mineral supplement and short-chain fructo-oligosaccharides on serum lipids in postmenopausal women.

PubMed

Cronin, Barbara E; Allsopp, Philip J; Slevin, Mary M; Magee, Pamela J; Livingstone, M Barbara E; Strain, J J; McSorley, Emeir M

2016-02-28

Recent literature suggests that Ca supplements have adverse effects on cardiovascular health. The effects of a Ca-rich supplement administered alone or in combination with short-chain fructo-oligosaccharides (scFOS) on serum lipids in postmenopausal women were examined using secondary data from a 24-month double-blind randomised controlled study. A total of 300 postmenopausal women were randomly assigned to daily supplements of 800 mg of Ca (2·4 g Aquamin) (Ca), 800 mg of Ca with 3 g of scFOS (CaFOS) or control (maltodextrin) (MD). A full lipid profile, body composition, blood pressure and a range of cytokines were measured at baseline and after 24 months. Intention-to-treat ANCOVA assessed treatment effects between the groups. A significant time-by-treatment effect was observed for LDL and total cholesterol for the Ca and CaFOS groups, with both groups having lower LDL and total cholesterol concentrations compared with MD after 24 months. The control group had mean (5·2 mmol/l) total cholesterol concentrations above the normal range (≤ 5 mmol/l) at 24 months, whereas values remained within the normal range in the treatment groups. There was no significant treatment effect on HDL-cholesterol, TAG, body composition, blood pressure or cytokine concentrations at 24 months, with the exception of IL-4, where there was a significant increase in the CaFOS group compared with the placebo. This study demonstrates a lipid-lowering effect of both the Ca-rich supplement alone and the supplement with scFOS. At the 4-year follow-up, there was no significant difference between the groups for reported diagnosed cardiovascular conditions.

Covalently Linked Tandem Lesions in DNA

PubMed Central

Patrzyc, Helen B.; Dawidzik, Jean B.; Budzinski, Edwin E.; Freund, Harold G.; Wilton, John H.; Box, Harold C.

2013-01-01

Reactive oxygen species (ROS) generate a type of DNA damage called tandem lesions, two adjacent nucleotides both modified. A subcategory of tandem lesions consists of adjacent nucleotides linked by a covalent bond. Covalently linked tandem lesions generate highly characteristic liquid chromotography-tandem mass spectrometry (LC-MS/MS) elution profiles. We have used this property to comprehensively survey X-irradiated DNA for covalently linked tandem lesions. A total of 15 tandem lesions were detected in DNA irradiated in deoxygenated aqueous solution, five tandem lesions were detected in DNA that was irradiated in oxygenated solution. PMID:23106212

Chromium-rich lawsonite in high-Cr eclogites from the Făgăras Massif (South Carpathians)

NASA Astrophysics Data System (ADS)

Negulescu, E.; Săbău, G.

2012-12-01

Lawsonite is a relatively rare phase in natural rocks, because of its thermal decomposition during exhumation, and Cr-bearing lawsonite being restricted to only a few occurrences worldwide. Here we report Cr-lawsonite in eclogites hosted in a medium-grade metamorphic complex. Several high-Cr eclogite lenses occur in the Topolog Complex (Făgăras Massif) of dominantly gneissic-amphibolitic composition. High Cr contents are the result of emerald-green mm-sized nodules containing Cr-rich minerals, embedded in a gray-green matrix of kyanite, clinopyroxene, garnet, amphibole, zoisite, and rutile. Garnets occur as porphyroblasts or in coronas around clinopyroxene aggregates probably replacing former magmatic pyroxene. Relict gabbroic textures (sometimes pegmatoid) and whole rock geochemistry indicate a gabbroic cumulate origin. The REE pattern, displaying a slight positive Eu anomaly and a tea spoon-shaped LREE depletion is also indicative of a cumulate origin, as also noted by Pe Piper & Piper (2002) for the Othrys gabbro (as well as others in the Vourinos and Pindos ophiolitic suites) with the same unusual REE-pattern. The emerald-green Cr-rich nodules are unevenly distributed in the rock, and always enclosed in Cr-rich clinopyroxenes (up to 5.46% Cr2O3) which may exhibit Cr-diffusion haloes towards normal Cr-free matrix pyroxene. The nodules consist of diablastic chromite, rutile and Cr-rich kyanite of up to 15.67 wt% Cr2O3, Cr-bearing epidote, to which Cr-rich staurolite (up to 10.45% Cr2O3; XMg up to 0.68) and Cr-rich lawsonite (up to 9.17% Cr2O3) may exceptionally associate. Cr concentrations in kyanite and lawsonite are, to our knowledge, the highest reported so far. Cr-lawsonite was identified in a single sample, as small single phase inclusions armoured in Cr-kyanite. Equilibrium PT-conditions of 2.6 GPa and 610o C were derived from the garnet-mantled clinopyroxene aggregates using multi-equilibria calculation with the PTGIBBS routine of Brandelik & Massonne

Monitoring of Sea Ice Dynamic by Means of ERS-Envisat Tandem Cross-Interferometry

NASA Astrophysics Data System (ADS)

Pasquali, Paolo; Cantone, Alessio; Barbieri, Massimo; Engdahl, Marcus

2010-03-01

The interest in the monitoring of sea ice masses has increased greatly over the past decades for a variety of reasons. These include:- Navigation in northern latitude waters;- transportation of petroleum;- exploitation of mineral deposits in the Arctic, and- the use of icebergs as a source of fresh water.The availability of ERS-Envisat 28minute tandem acquisitions from dedicated campaigns, covering large areas in the northern latitudes with large geometrical baseline and very short temporal separation, allows the precise estimation of sea ice displacement fields with an accuracy that cannot be obtained on large scale from any other instrument. This article presents different results of sea ice dynamic monitoring over northern Canada obtained within the "ERS-Envisat Tandem Cross-Interferometry Campaigns: CInSAR processing and studies over extended areas" project from data acquired during the 2008-2009 Tandem campaign..

Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue*

PubMed Central

Plubell, Deanna L.; Wilmarth, Phillip A.; Zhao, Yuqi; Fenton, Alexandra M.; Minnier, Jessica; Reddy, Ashok P.; Klimek, John; Yang, Xia; David, Larry L.

2017-01-01

The lack of high-throughput methods to analyze the adipose tissue protein composition limits our understanding of the protein networks responsible for age and diet related metabolic response. We have developed an approach using multiple-dimension liquid chromatography tandem mass spectrometry and extended multiplexing (24 biological samples) with tandem mass tags (TMT) labeling to analyze proteomes of epididymal adipose tissues isolated from mice fed either low or high fat diet for a short or a long-term, and from mice that aged on low versus high fat diets. The peripheral metabolic health (as measured by body weight, adiposity, plasma fasting glucose, insulin, triglycerides, total cholesterol levels, and glucose and insulin tolerance tests) deteriorated with diet and advancing age, with long-term high fat diet exposure being the worst. In response to short-term high fat diet, 43 proteins representing lipid metabolism (e.g. AACS, ACOX1, ACLY) and red-ox pathways (e.g. CPD2, CYP2E, SOD3) were significantly altered (FDR < 10%). Long-term high fat diet significantly altered 55 proteins associated with immune response (e.g. IGTB2, IFIT3, LGALS1) and rennin angiotensin system (e.g. ENPEP, CMA1, CPA3, ANPEP). Age-related changes on low fat diet significantly altered only 18 proteins representing mainly urea cycle (e.g. OTC, ARG1, CPS1), and amino acid biosynthesis (e.g. GMT, AKR1C6). Surprisingly, high fat diet driven age-related changes culminated with alterations in 155 proteins involving primarily the urea cycle (e.g. ARG1, CPS1), immune response/complement activation (e.g. C3, C4b, C8, C9, CFB, CFH, FGA), extracellular remodeling (e.g. EFEMP1, FBN1, FBN2, LTBP4, FERMT2, ECM1, EMILIN2, ITIH3) and apoptosis (e.g. YAP1, HIP1, NDRG1, PRKCD, MUL1) pathways. Using our adipose tissue tailored approach we have identified both age-related and high fat diet specific proteomic signatures highlighting a pronounced involvement of arginine metabolism in response to advancing age

Achieving 12.8% Efficiency by Simultaneously Improving Open-Circuit Voltage and Short-Circuit Current Density in Tandem Organic Solar Cells.

PubMed

Qin, Yunpeng; Chen, Yu; Cui, Yong; Zhang, Shaoqing; Yao, Huifeng; Huang, Jiang; Li, Wanning; Zheng, Zhong; Hou, Jianhui

2017-06-01

Tandem organic solar cells (TOSCs), which integrate multiple organic photovoltaic layers with complementary absorption in series, have been proved to be a strong contender in organic photovoltaic depending on their advantages in harvesting a greater part of the solar spectrum and more efficient photon utilization than traditional single-junction organic solar cells. However, simultaneously improving open circuit voltage (V oc ) and short current density (J sc ) is a still particularly tricky issue for highly efficient TOSCs. In this work, by employing the low-bandgap nonfullerene acceptor, IEICO, into the rear cell to extend absorption, and meanwhile introducing PBDD4T-2F into the front cell for improving V oc , an impressive efficiency of 12.8% has been achieved in well-designed TOSC. This result is also one of the highest efficiencies reported in state-of-the-art organic solar cells. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults.

PubMed

Tap, Julien; Furet, Jean-Pierre; Bensaada, Martine; Philippe, Catherine; Roth, Hubert; Rabot, Sylvie; Lakhdari, Omar; Lombard, Vincent; Henrissat, Bernard; Corthier, Gérard; Fontaine, Eric; Doré, Joël; Leclerc, Marion

2015-12-01

Gut microbiota richness and stability are important parameters in host-microbe symbiosis. Diet modification, notably using dietary fibres, might be a way to restore a high richness and stability in the gut microbiota. In this work, during a 6-week nutritional trial, 19 healthy adults consumed a basal diet supplemented with 10 or 40 g dietary fibre per day for 5 days, followed by 15-day washout periods. Fecal samples were analysed by a combination of 16S rRNA gene pyrosequencing, intestinal cell genotoxicity assay, metatranscriptomics sequencing approach and short-chain fatty analysis. This short-term change in the dietary fibre level did not have the same impact for all individuals but remained significant within each individual gut microbiota at genus level. Higher microbiota richness was associated with higher microbiota stability upon increased dietary fibre intake. Increasing fibre modulated the expression of numerous microbiota metabolic pathways such as glycan metabolism, with genes encoding carbohydrate-active enzymes active on fibre or host glycans. High microbial richness was also associated with high proportions of Prevotella and Coprococcus species and high levels of caproate and valerate. This study provides new insights on the role of gut microbial richness in healthy adults upon dietary changes and host microbes' interaction. © 2015 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging

PubMed Central

Ma, Ze-Qiang; Chambers, Matthew C.; Ham, Amy-Joan L.; Cheek, Kristin L.; Whitwell, Corbin W.; Aerni, Hans-Rudolf; Schilling, Birgit; Miller, Aaron W.; Caprioli, Richard M.; Tabb, David L.

2011-01-01

In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools. Despite recent improvements in identification algorithms, a significant number of high quality spectra remain unidentified for various reasons. Here we present ScanRanker, an open-source tool that evaluates the quality of tandem mass spectra via sequence tagging with reliable performance in data from different instruments. The superior performance of ScanRanker enables it not only to find unassigned high quality spectra that evade identification through database search, but also to select spectra for de novo sequencing and cross-linking analysis. In addition, we demonstrate that the distribution of ScanRanker scores predicts the richness of identifiable spectra among multiple LC-MS/MS runs in an experiment, and ScanRanker scores assist the process of peptide assignment validation to increase confident spectrum identifications. The source code and executable versions of ScanRanker are available from http://fenchurch.mc.vanderbilt.edu. PMID:21520941

Real-Time Study of the Interaction between G-Rich DNA Oligonucleotides and Lead Ion on DNA Tetrahedron-Functionalized Sensing Platform by Dual Polarization Interferometry.

PubMed

Wang, Shuang; Lu, Shasha; Zhao, Jiahui; Huang, Jianshe; Yang, Xiurong

2017-11-29

G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb 2+ . The oriented immobilization of probes greatly decreased the spatial hindrance effect and improved the accessibility of the probes to the Pb 2+ ions. Through real-time monitoring of the whole formation process of the G-quadruplex, we speculated that the probes on the tetrahedron platform initially stood on the sensing surface with a random coil conformation, then the G-rich ssDNA preliminarily formed unstable G-quartets by H-bonding and cation binding, subsequently forming a completely folded and stable quadruplex structure through relatively slow strand rearrangements. On the basis of these studies, we also developed a novel sensing platform for the specific and sensitive determination of Pb 2+ and its chelating agent ethylenediaminetetraacetic acid. This study not only provides a proof-of-concept for conformational dynamics of G-quadruplex-related drugs and pathogenes, but also enriches the biosensor tools by combining nanomaterial with interfaces technique.

All-silicon tandem solar cells: Practical limits for energy conversion and possible routes for improvement

NASA Astrophysics Data System (ADS)

Jia, Xuguang; Puthen-Veettil, Binesh; Xia, Hongze; Yang, Terry Chien-Jen; Lin, Ziyun; Zhang, Tian; Wu, Lingfeng; Nomoto, Keita; Conibeer, Gavin; Perez-Wurfl, Ivan

2016-06-01

Silicon nanocrystals (Si NCs) embedded in a dielectric matrix is regarded as one of the most promising materials for the third generation photovoltaics, owing to their tunable bandgap that allows fabrication of optimized tandem devices. Previous work has demonstrated fabrication of Si NCs based tandem solar cells by sputter-annealing of thin multi-layers of silicon rich oxide and SiO2. However, these device efficiencies were much lower than expected given that their theoretical values are much higher. Thus, it is necessary to understand the practical conversion efficiency limits for these devices. In this article, practical efficiency limits of Si NC based double junction tandem cells determined by fundamental material properties such as minority carrier, mobility, and lifetime are investigated. The practical conversion efficiency limits for these devices are significantly different from the reported efficiency limits which use Shockley-Queisser assumptions. Results show that the practical efficiency limit of a double junction cell (1.6 eV Si NC top cell and a 25% efficient c-Si PERL cell as the bottom cell) is 32%. Based on these results suggestions for improvement to the performance of Si nanocrystal based tandem solar cells in terms of the different parameters that were simulated are presented.

Orthogonal tandem catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lohr, Tracy L.; Marks, Tobin J.

2015-05-20

Tandem catalysis is a growing field that is beginning to yield important scientific and technological advances toward new and more efficient catalytic processes. 'One-pot' tandem reactions, where multiple catalysts and reagents, combined in a single reaction vessel undergo a sequence of precisely staged catalytic steps, are highly attractive from the standpoint of reducing both waste and time. Orthogonal tandem catalysis is a subset of one-pot reactions in which more than one catalyst is used to promote two or more mechanistically distinct reaction steps. This Perspective summarizes and analyses some of the recent developments and successes in orthogonal tandem catalysis, withmore » particular focus on recent strategies to address catalyst incompatibility. We also highlight the concept of thermodynamic leveraging by coupling multiple catalyst cycles to effect challenging transformations not observed in single-step processes, and to encourage application of this technique to energetically unfavourable or demanding reactions.« less

Tandem Repeats in Proteins: Prediction Algorithms and Biological Role.

PubMed

Pellegrini, Marco

2015-01-01

Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR.

A systematic tandem mass spectrometric study of anion attachment for improved detection and acidity evaluation of nitrogen-rich energetic compounds.

PubMed

Gaiffe, Gabriel; Bridoux, Maxime C; Costanza, Christine; Cole, Richard B

2018-01-01

The development of rapid, efficient, and reliable detection methods for the characterization of energetic compounds is of high importance to security forces concerned with terrorist threats. With a mass spectrometric approach, characteristic ions can be produced by attaching anions to analyte molecules in the negative ion mode of electrospray ionization mass spectrometry (ESI-MS). Under optimized conditions, formed anionic adducts can be detected with higher sensitivities as compared with the deprotonated molecules. Fundamental aspects pertaining to the formation of anionic adducts of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), 1,3,5-trinitro-1,3,5-triazinane (RDX), pentaerythritol tetranitrate (PETN), nitroglycerin (NG), and 1,3,5-trinitroso-1,3,5-triazinane energetic (R-salt) compounds using various anions have been systematically studied by ESI-MS and ESI tandem mass spectrometry (collision-induced dissociation) experiments. Bracketing method results show that the gas-phase acidities of PETN, RDX, and HMX fall between those of HF and acetic acid. Moreover, PETN and RDX are each less acidic than HMX in the gas phase. Nitroglycerin was found to be the most acidic among the nitrogen-rich explosives studied. The ensemble of bracketing results allows the construction of the following ranking of gas-phase acidities: PETN (1530-1458 kJ/mol) > RDX (approximately 1458 kJ/mol) > HMX (approximately 1433 kJ/mol) > nitroglycerin (1427-1327.8 kJ/mol). Copyright © 2017 John Wiley & Sons, Ltd.

G2019S leucine-rich repeat kinase 2 causes uncoupling protein-mediated mitochondrial depolarization

PubMed Central

Papkovskaia, Tatiana D.; Chau, Kai-Yin; Inesta-Vaquera, Francisco; Papkovsky, Dmitri B.; Healy, Daniel G.; Nishio, Koji; Staddon, James; Duchen, Michael R.; Hardy, John; Schapira, Anthony H.V.; Cooper, J. Mark

2012-01-01

The G2019S leucine rich repeat kinase 2 (LRRK2) mutation is the most common genetic cause of Parkinson's disease (PD), clinically and pathologically indistinguishable from idiopathic PD. Mitochondrial abnormalities are a common feature in PD pathogenesis and we have investigated the impact of G2019S mutant LRRK2 expression on mitochondrial bioenergetics. LRRK2 protein expression was detected in fibroblasts and lymphoblasts at levels higher than those observed in the mouse brain. The presence of G2019S LRRK2 mutation did not influence LRRK2 expression in fibroblasts. However, the expression of the G2019S LRRK2 mutation in both fibroblast and neuroblastoma cells was associated with mitochondrial uncoupling. This was characterized by decreased mitochondrial membrane potential and increased oxygen utilization under basal and oligomycin-inhibited conditions. This resulted in a decrease in cellular ATP levels consistent with compromised cellular function. This uncoupling of mitochondrial oxidative phosphorylation was associated with a cell-specific increase in uncoupling protein (UCP) 2 and 4 expression. Restoration of mitochondrial membrane potential by the UCP inhibitor genipin confirmed the role of UCPs in this mechanism. The G2019S LRRK2-induced mitochondrial uncoupling and UCP4 mRNA up-regulation were LRRK2 kinase-dependent, whereas endogenous LRRK2 levels were required for constitutive UCP expression. We propose that normal mitochondrial function was deregulated by the expression of G2019S LRRK2 in a kinase-dependent mechanism that is a modification of the normal LRRK2 function, and this leads to the vulnerability of selected neuronal populations in PD. PMID:22736029

Photosynthetic and Biochemical Changes in Response to Short Interval High ``g'' Exposure in Wheat

NASA Astrophysics Data System (ADS)

Dixit, Jyotsana; Vidyasagar, Pandit; Jagtap, Sagar; Kamble, Shailendra

We have investigated the effect of short interval post imbibition high “g” exposure on wheat seeds (Triticum aestivum var.Lok-1) by evaluating the photosynthetic performance, chlorophyll “a” fluorescence biochemical indices and antioxidant response. Imbibed wheat seeds were exposed to high “g” ranging from 500 g to 2500 g for 10 min, allowed to germinate and grown for 5 days under normal gravity i.e. 1 g. Chlorophyll “a” fluorescence transient was examined in wheat seedling raised from hyper gravity treated seeds. Fv/Fm, PI, Fv/Fo decreased in high “g” treated seeds compared to control. Photosynthetic performance indices such as Transpiration rate, Stomatal conductance, Net photosynthetic rate, Intracellular CO2 concentration, Intrinsic water use efficiency also declined in wheat seedlings raised from High “g” treated seeds suggesting that high g reduces efficiency of photosynthesis in wheat seedlings. Results of Biochemical analysis showed reduced alpha- amylase activity in wheat seeds subjected to high “g” ranging from 500 g to 2500 g in a magnitude dependent manner. Decline in enzyme activity was positively correlated with higher starch content and lower reducing sugars in high “g” exposed wheat seeds. This possibly explains the reduced percent germination and growth in response to high “g”. Antioxidant enzyme activity (CAT and POX) significantly increased as a result of hypergravity exposure In conclusion, short interval high “g” exposure results in reduced growth and photosynthetic activity in wheat seedlings.

Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA

PubMed Central

Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

2017-01-01

Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. PMID:28600436

Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues.

PubMed

Barallon, Rita; Bauer, Steven R; Butler, John; Capes-Davis, Amanda; Dirks, Wilhelm G; Elmore, Eugene; Furtado, Manohar; Kline, Margaret C; Kohara, Arihiro; Los, Georgyi V; MacLeod, Roderick A F; Masters, John R W; Nardone, Mark; Nardone, Roland M; Nims, Raymond W; Price, Paul J; Reid, Yvonne A; Shewale, Jaiprakash; Sykes, Gregory; Steuer, Anton F; Storts, Douglas R; Thomson, Jim; Taraporewala, Zenobia; Alston-Roberts, Christine; Kerrigan, Liz

2010-10-01

Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using short tandem repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues.

Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues

PubMed Central

Barallon, Rita; Bauer, Steven R.; Butler, John; Capes-Davis, Amanda; Dirks, Wilhelm G.; Furtado, Manohar; Kline, Margaret C.; Kohara, Arihiro; Los, Georgyi V.; MacLeod, Roderick A. F.; Masters, John R. W.; Nardone, Mark; Nardone, Roland M.; Nims, Raymond W.; Price, Paul J.; Reid, Yvonne A.; Shewale, Jaiprakash; Sykes, Gregory; Steuer, Anton F.; Storts, Douglas R.; Thomson, Jim; Taraporewala, Zenobia; Alston-Roberts, Christine; Kerrigan, Liz

2010-01-01

Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using short tandem repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues. PMID:20614197

Comparative Transcriptomic Analysis of the Response of Dunaliella acidophila (Chlorophyta) to Short-Term Cadmium and Chronic Natural Metal-Rich Water Exposures.

PubMed

Puente-Sánchez, Fernando; Olsson, Sanna; Aguilera, Angeles

2016-10-01

Heavy metals are toxic compounds known to cause multiple and severe cellular damage. However, acidophilic extremophiles are able to cope with very high concentrations of heavy metals. This study investigated the stress response under natural environmental heavy metal concentrations in an acidophilic Dunaliella acidophila. We employed Illumina sequencing for a de novo transcriptome assembly and to identify changes in response to high cadmium concentrations and natural metal-rich water. The photosynthetic performance was also estimated by pulse amplitude-modulated (PAM) fluorescence. Transcriptomic analysis highlights a number of processes mainly related to a high constitutive expression of genes involved in oxidative stress and response to reactive oxygen species (ROS), even in the absence of heavy metals. Photosynthetic activity seems to be unaltered under short-term exposition to Cd and chronic exposure to natural metal-rich water, probably due to an increase in the synthesis of structural photosynthetic components preserving their functional integrity. An overrepresentation of Gene Ontology (GO) terms related to metabolic activities, transcription, and proteosomal catabolic process was observed when D. acidophila grew under chronic exposure to natural metal-rich water. GO terms involved in carbohydrate metabolic process, reticulum endoplasmic and Golgi bodies, were also specifically overrepresented in natural metal-rich water library suggesting an endoplasmic reticulum stress response.

Achieving 15% Tandem Polymer Solar Cells

DTIC Science & Technology

2015-06-23

solar cell structures – both polymer only and hybrid tandem cells to constantly pushing the envelope of solution processed solar cell ...performance – 11.6% polymer tandem cell , 7% transparent tandem polymer cell , and over 10% PCE hybrid tandem solar cells were achieved. In addition, AFOSR’s...final support also enabled us to explore novel hybrid perovskite solar cells in depth. For example, single junction cell efficiency

Enhanced kidney stone fragmentation by short delay tandem conventional and modified lithotriptor shock waves: a numerical analysis.

PubMed

Tham, Leung-Mun; Lee, Heow Pueh; Lu, Chun

2007-07-01

We evaluated the effectiveness of modified lithotriptor shock waves using computer models. Finite element models were used to simulate the propagation of lithotriptor shock waves in human renal calculi in vivo. Kidney stones were assumed to be spherical, homogeneous, isotropic and linearly elastic, and immersed in a continuum fluid. Single and tandem shock wave pulses modified to intensify the collapse of cavitation bubbles near the stone surface to increase fragmentation efficiency and suppress the expansion of intraluminal bubbles for decreased vascular injury were analyzed. The effectiveness of the modified shock waves was assessed by comparing the states of loading in the renal calculi induced by these shock waves to those produced by conventional shock waves. Our numerical simulations revealed that modified shock waves produced marginally lower stresses in spherical renal calculi than those produced by conventional shock waves. Tandem pulses of conventional or modified shock waves produced peak stresses in the front and back halves of the renal calculi. However, the single shock wave pulses generated significant peak stresses in only the back halves of the renal calculi. Our numerical simulations suggest that for direct stress wave induced fragmentation modified shock waves should be as effective as conventional shock waves for fragmenting kidney stones. Also, with a small interval of 20 microseconds between the pulses tandem pulse lithotripsy using modified or conventional shock waves could be considerably more effective than single pulse lithotripsy for fragmenting kidney stones.

Linking Y-chromosomal short tandem repeat loci to human male impulsive aggression.

PubMed

Yang, Chun; Ba, Huajie; Cao, Yin; Dong, Guoying; Zhang, Shuyou; Gao, Zhiqin; Zhao, Hanqing; Zhou, Xianju

2017-11-01

Men are more susceptible to impulsive behavior than women. Epidemiological studies revealed that the impulsive aggressive behavior is affected by genetic factors, and the male-specific Y chromosome plays an important role in this behavior. In this study, we investigated the association between the impulsive aggressive behavior and Y-chromosomal short tandem repeats (Y-STRs) loci. The collected biologic samples from 271 offenders with impulsive aggressive behavior and 492 healthy individuals without impulsive aggressive behavior were amplified by PowerPlex R Y23 PCR System and the resultant products were separated by electrophoresis and further genotyped. Then, comparisons in allele and haplotype frequencies of the selected 22 Y-STRs were made in the two groups. Our results showed that there were significant differences in allele frequencies at DYS448 and DYS456 between offenders and controls ( p  < .05). Univariate analysis further revealed significant frequency differences for alleles 18 and 22 at DYS448 (0.18 vs 0.27, compared to the controls, p  = .003, OR=0.57,95% CI=0.39-0.82; 0.03 vs 0.01, compared to the controls, p  = .003, OR=7.45, 95% CI=1.57-35.35, respectively) and for allele 17 at DYS456 (0.07 vs 0.14, compared to the controls, p  = .006, OR=0.48, 95% CI =0.28-0.82) between two groups. Interestingly, the frequency of haploid haplotype 22-15 on the DYS448-DYS456 (DYS448-DYS456-22-15) was significantly higher in offenders than in controls (0.033 vs 0.004, compared to the control, p  = .001, OR = 8.42, 95%CI =1.81-39.24). Moreover, there were no significant differences in allele frequencies of other Y-STRs loci between two groups. Furthermore, the unconditional logistic regression analysis confirmed that alleles 18 and 22 at DYS448 and allele 17 at DYS456 are associated with male impulsive aggression. However, the DYS448-DYS456-22-15 is less related to impulsive aggression. Our results suggest a link between Y-chromosomal allele types and male

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

PubMed

Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

2007-07-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.

Fifteen non-CODIS autosomal short tandem repeat loci multiplex data from nine population groups living in Taiwan.

PubMed

Hwa, Hsiao-Lin; Chang, Yih-Yuan; Lee, James Chun-I; Lin, Chun-Yen; Yin, Hsiang-Yi; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

2012-07-01

The analysis of autosomal short tandem repeat (STR) loci is a powerful tool in forensic genetics. We developed a multiplex system in which 15 non-Combined DNA Index System autosomal STRs (D3S1744, D4S2366, D8S1110, D10S2325, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 1,098 unrelated subjects of nine population groups living in Taiwan, including Taiwanese Han, indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, Thais, Vietnamese, Indonesians, and Caucasians, were collected and analyzed using this system. The distributions of the allelic frequencies and the forensic parameters of each population group were presented. The combined discrimination power and the combined power of exclusion were high in all population groups tested in this study. A multidimensional scaling plot of these nine population groups based on the Reynolds' genetic distances calculated from 15 autosomal STRs was constructed, and the genetic substructure in this area was presented. In conclusion, this 15 autosomal STR multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing in different populations.

An Ultra-High Discrimination Y Chromosome Short Tandem Repeat Multiplex DNA Typing System

PubMed Central

Hanson, Erin K.; Ballantyne, Jack

2007-01-01

In forensic casework, Y chromosome short tandem repeat markers (Y-STRs) are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12–17 loci are currently used in forensic casework (Promega's PowerPlex® Y and Applied Biosystems' AmpFlSTR® Yfiler®). Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used ‘core’ Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD) multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572) indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR® Yfiler® kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary

Advanced astigmatism-corrected tandem Wadsworth mounting for small-scale spectral broadband imaging spectrometer.

PubMed

Lei, Yu; Lin, Guan-yu

2013-01-01

Tandem gratings of double-dispersion mount make it possible to design an imaging spectrometer for the weak light observation with high spatial resolution, high spectral resolution, and high optical transmission efficiency. The traditional tandem Wadsworth mounting is originally designed to match the coaxial telescope and large-scale imaging spectrometer. When it is used to connect the off-axis telescope such as off-axis parabolic mirror, it presents lower imaging quality than to connect the coaxial telescope. It may also introduce interference among the detector and the optical elements as it is applied to the short focal length and small-scale spectrometer in a close volume by satellite. An advanced tandem Wadsworth mounting has been investigated to deal with the situation. The Wadsworth astigmatism-corrected mounting condition for which is expressed as the distance between the second concave grating and the imaging plane is calculated. Then the optimum arrangement for the first plane grating and the second concave grating, which make the anterior Wadsworth condition fulfilling each wavelength, is analyzed by the geometric and first order differential calculation. These two arrangements comprise the advanced Wadsworth mounting condition. The spectral resolution has also been calculated by these conditions. An example designed by the optimum theory proves that the advanced tandem Wadsworth mounting performs excellently in spectral broadband.

The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo.

PubMed

Ribeyre, Cyril; Lopes, Judith; Boulé, Jean-Baptiste; Piazza, Aurèle; Guédin, Aurore; Zakian, Virginia A; Mergny, Jean-Louis; Nicolas, Alain

2009-05-01

In budding yeast, the Pif1 DNA helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. Here, we provide evidence for a new Pif1 function by demonstrating that its absence promotes genetic instability of alleles of the G-rich human minisatellite CEB1 inserted in the Saccharomyces cerevisiae genome, but not of other tandem repeats. Inactivation of other DNA helicases, including Sgs1, had no effect on CEB1 stability. In vitro, we show that CEB1 repeats formed stable G-quadruplex (G4) secondary structures and the Pif1 protein unwinds these structures more efficiently than regular B-DNA. Finally, synthetic CEB1 arrays in which we mutated the potential G4-forming sequences were no longer destabilized in pif1Delta cells. Hence, we conclude that CEB1 instability in pif1Delta cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences.

Determination of alcohol sulfates and alcohol ethoxysulfates in marine and river sediments using liquid chromatography-tandem mass spectrometry.

PubMed

Fernández-Ramos, C; Ballesteros, O; Blanc, R; Zafra-Gómez, A; Camino-Sánchez, F J; Navalón, A; Vílchez, J L

2013-10-15

A novel and successful method has been developed for the identification and quantification of alcohol sulfates (AS) homologues and alcohol ethoxysulfates (AES) ethoxymers in marine and river sediment samples. The method involves the extraction of 5.00 g of dry sample with methanol using pressurized liquid extraction (PLE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). 2-Octylbenzene sulfonic acid sodium salt (2ØC8-LAS) was used as internal standard. The analytical methods were applied to marine sediments collected from the coast of Almeria (South-east Spain) and river sediments collected from the Monachil river (Granada, South-east Spain). For AS homologues, the found limits of detection were 0.04-0.08 μg g(-1) for marine and river sediments. For AES ethoxymers, the found limits of detection were 0.03-0.09 μg g(-1) and 0.06-0.22 μg g(-1) for marine and river sediments, respectively. The highest concentrations of AS and AES were found in river sediment samples. Significant differences were also observed between the behavior of short-chain compounds (C12) and long-chain compounds (C14 to C18). The influence of the physic-chemical properties of water on the occurrence of these compounds was also evaluated, and differences between long- and short-chain compounds were also observed. Additionally, principal components analyses were carried out in order to study the relationship between variables and to evaluate the sources of data variability and behavior patterns. Finally, important conclusions were drawn regarding the environmental behavior of AS and AES. Copyright © 2013 Elsevier B.V. All rights reserved.

Chemistry of the organic-rich hot core G327.3-0.6

NASA Technical Reports Server (NTRS)

Gibb, E.; Nummelin, A.; Irvine, W. M.; Whittet, D. C.; Bergman, P.; Ferris, J. P. (Principal Investigator)

2000-01-01

We present gas-phase abundances of species found in the organic-rich hot core G327.3-0.6. The data were taken with the Swedish-ESO Submillimetre Telescope (SEST). The 1-3 mm spectrum of this source is dominated by emission features of nitrile species and saturated organics, with abundances greater than those found in many other hot cores, including Sgr B2 and OMC-1. Population diagram analysis indicates that many species (CH3CN, C2H3CN, C2H5CN, CH3OH, etc.) have hot components that originate in a compact (2") region. Gas-phase chemical models cannot reproduce the high abundances of these molecules found in hot cores, and we suggest that they originate from processing and evaporation of icy grain mantle material. In addition, we report the first detection of vibrationally excited ethyl cyanide and the first detection of methyl mercaptan (CH3SH) outside the Galactic center.

Short exposure to a diet rich in both fat and sugar or sugar alone impairs place, but not object recognition memory in rats.

PubMed

Beilharz, Jessica E; Maniam, Jayanthi; Morris, Margaret J

2014-03-01

High energy diets have been shown to impair cognition however, the rapidity of these effects, and the dietary component/s responsible are currently unclear. We conducted two experiments in rats to examine the effects of short-term exposure to a diet rich in sugar and fat or rich in sugar on object (perirhinal-dependent) and place (hippocampal-dependent) recognition memory, and the role of inflammatory mediators in these responses. In Experiment 1, rats fed a cafeteria style diet containing chow supplemented with lard, cakes, biscuits, and a 10% sucrose solution performed worse on the place, but not the object recognition task, than chow fed control rats when tested after 5, 11, and 20 days. In Experiment 2, rats fed the cafeteria style diet either with or without sucrose and rats fed chow supplemented with sucrose also performed worse on the place, but not the object recognition task when tested after 5, 11, and 20 days. Rats fed the cafeteria diets consumed five times more energy than control rats and exhibited increased plasma leptin, insulin and triglyceride concentrations; these were not affected in the sucrose only rats. Rats exposed to sucrose exhibited both increased hippocampal inflammation (TNF-α and IL-1β mRNA) and oxidative stress, as indicated by an upregulation of NRF1 mRNA compared to control rats. In contrast, these markers were not significantly elevated in rats that received the cafeteria diet without added sucrose. Hippocampal BDNF and neuritin mRNA were similar across all groups. These results show that relatively short exposures to diets rich in both fat and sugar or rich in sugar, impair hippocampal-dependent place recognition memory prior to the emergence of weight differences, and suggest a role for oxidative stress and neuroinflammation in this impairment. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

TANDEM: matching proteins with tandem mass spectra.

PubMed

Craig, Robertson; Beavis, Ronald C

2004-06-12

Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.

Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA.

PubMed

Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

2017-09-01

Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77-0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea.

PubMed

Moon, Seo Hyun; Jang, Yoon-Jeong; Han, Myun Soo; Cho, Myung-Haing

2016-09-30

Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10(-)⁵ for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.

[Determination of aflatoxin B1, B2, G1, G2 in armeniacae semen amarum by high-performance liquid chromatography-tandem mass spectrometry].

PubMed

Zheng, Run-Sheng; Xu, Hui; Wang, Wen-Li; Zhan, Ruo-Ting; Chen, Wei-Wen

2013-10-01

A simple, rapid and cost-effective high-performance liquid chromatography-tandem mass spectrometry (LC-MS/ MS) method was established for simultaneous determination of aflatoxins (AFB1, AFB2, AFG1, AFG2) in Armeniacae Semen Amarum and the application was performance in 11 samples collected from different markets, medical stores and hospitals. The sample was extracted with 84% acetonitrile/water and 250 microL extraction was directly injected into a LC-MS/MS system without further purification procedure after being redissolved with methanol. The LC separation was performed on a C18 column with a linear gradient elution program of 4 mmol x L(-1) NH4 Ac-0.1% formic acid solution and menthol as the mobile phase. Selected reaction monitoring (SRM) was used for selective determination of the four aflatoxins on a triple quadruple mass spectrometer, which was operated in positive ionization modes. All the four aflatoxins showed a good linear relationship with r > 0.999 0, the average recoveries were between 87.88% and 102.9% and the matrix effect was ranged from 90.71% to 99.30% in low, intermediate and high levels. Furthermore, the higher recovery was obtained by the method reported in this study, comparing to the cleanup procedure with the Mycosep 226 purification column. Eleven samples collected were detected and the contamination levels of the AFB1 were between 1.590-2.340 microg x kg(-1) and the AF (B1 + B2 + G1 + G2) was ranged from 2.340 to 3.340 microg x kg(-1). In summary, the developed method was suitable to detect and screen AFB1, AFB2, AFG1, AFG2 in Armeniacae Semen Amarum.

Simultaneous determination of 24 polycyclic aromatic hydrocarbons in edible oil by tandem solid-phase extraction and gas chromatography coupled/tandem mass spectrometry.

PubMed

Xu, Ting; Tang, Hua; Chen, Dazhou; Dong, Haifeng; Li, Lei

2015-01-01

An efficient and fast tandem SPE method followed by GC/MS/MS has been developed for the determination and the quantification of 24 polycyclic aromatic hydrocarbons (PAHs) in edible oil. This method includes the monitoring of 15 + 1 PAHs designated as a priority by the European Union in their 2005/108/EC recommendation and 16 PAHs listed by the U. S. Environmental Protection Agency. The sample preparation procedures were based on SPE in which PAH-dedicated cartridges with molecularly imprinted polymers and graphitized carbon black were used in series. The novel tandem SPE combination of selective extraction and purification of light and heavy PAHs provided highly purified analytes. Identification and quantification of 24 target PAHs were performed using GC/MS/MS with the isotope dilution approaches using D-labeled and (13)C-labeled PAHs. The advantages of GC/MS/MS as compared to other detection methods include high sensitivity, selectivity, and interpretation ability. The method showed satisfactory linearity (R(2) > 0.998) over the range assayed (0.5-200 μg/kg); the LODs ranged from 0.03 to 0.6 μg/kg, and LOQs from 0.1 to 2.0 μg/kg. The recoveries using this method at three spiked concentration levels (2, 10, and 50 μg/kg) ranged from 56.8 to 117.7%. The RSD was lower than 12.7% in all cases. The proposed analytical method has been successfully applied for the analysis of the 24 PAHs in edible oil.

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

PubMed

Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean-Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta-Dorothee; Marian, Catalin; Gonzalez-Martin, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Haruo; Rangel Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev; Camacho, Rui; Fonseca, Nuno A

2011-09-01

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.

A liquid chromatography with tandem mass spectrometry method for simultaneous determination of UTL-5g and its metabolites in human plasma.

PubMed

Shaw, Jiajiu; Wiegand, Richard; Wu, Jianmei; Bao, Xun; Valeriote, Frederick; Li, Jing

2015-06-01

UTL-5g is a novel small-molecule TNF-α inhibitor under investigation as both a chemoprotective and radioprotective agent. Animal studies showed that pretreatment of UTL-5g protected kidney, liver, and platelets from cisplatin-induced toxicity. In addition, UTL-5g reduced liver and lung injuries induced by radiation in vivo. Although a number of preclinical studies have been conducted, a validated bioanalytical method for UTL-5g in human plasma has not been published. In this work, a sensitive and reproducible reverse-phase liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) assay was developed and validated for the determination of UTL-5g and its metabolites, 5-methylisoxazole-3-carboxylic acid (ISOX) and 2,4-dichloroaniline (DCA), in human plasma. The method involves a simple methanol precipitation step followed by injection of the supernatant onto a Waters 2695 HPLC system coupled with a Waters Quattro Micro™ triple quadrupole mass spectrometer. Chromatographic separation was accomplished using a Waters Nova-Pak C18 column maintained at 30°C, running at gradient mode with mobile phase consisting of 0.1% formic acid in water and 0.1% formic acid in methanol at a flow rate of 0.2mL/min. The analytes were monitored under positive electrospray ionization (ESI). Quantitation of these compounds in plasma was linear from 0.05 to 10μM. The lower limit of quantitation (LLOQ) was 0.05, 0.1, and 0.2μM for UTL-5g, ISOX and DCA, respectively. The accuracy and intra-and inter-day precisions were within the generally accepted criteria for bioanalytical method (<15%). This method provides a practical tool to measure and characterize the plasma concentration-time profiles for UTL-5g and its metabolites, ISOX and DCA. Copyright © 2015 Elsevier B.V. All rights reserved.

The data acquisition of OLGA II; An application of the PSI TANDEM system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jost, D.T.; Vermeulen, D.

1992-04-01

This paper describes the data acquisition of the on-line gas-chemistry apparatus (OLGA II). OLGA II is used to investigate the chemical behavior of volatile molecules of short lives isotopes. Special emphasis is given to the presentation of the PSI tandem data acquisition system used in these experiments. Time stamped event-by-event recording is used to follow radioactive decay chains.

Variant Alleles, Triallelic Patterns, and Point Mutations Observed in Nuclear Short Tandem Repeat Typing of Populations in Bosnia and Serbia

PubMed Central

Huel, René L. M.; Bašić, Lara; Madacki-Todorović, Kamelija; Smajlović, Lejla; Eminović, Izet; Berbić, Irfan; Miloš, Ana; Parsons, Thomas J.

2007-01-01

Aim To present a compendium of off-ladder alleles and other genotyping irregularities relating to rare/unexpected population genetic variation, observed in a large short tandem repeat (STR) database from Bosnia and Serbia. Methods DNA was extracted from blood stain cards relating to reference samples from a population of 32 800 individuals from Bosnia and Serbia, and typed using Promega’s PowerPlex®16 STR kit. Results There were 31 distinct off-ladder alleles were observed in 10 of the 15 STR loci amplified from the PowerPlex®16 STR kit. Of these 31 alleles, 3 have not been previously reported. Furthermore, 16 instances of triallelic patterns were observed in 9 of the 15 loci. Primer binding site mismatches that affected amplification were observed in two loci, D5S818 and D8S1179. Conclusion Instances of deviations from manufacturer’s allelic ladders should be expected and caution taken to properly designate the correct alleles in large DNA databases. Particular care should be taken in kinship matching or paternity cases as incorrect designation of any of these deviations from allelic ladders could lead to false exclusions. PMID:17696304

Structure and Function of the Two Tandem WW Domains of the Pre-mRNA Splicing Factor FBP21 (Formin-binding Protein 21)*

PubMed Central

Huang, Xiaojuan; Beullens, Monique; Zhang, Jiahai; Zhou, Yi; Nicolaescu, Emilia; Lesage, Bart; Hu, Qi; Wu, Jihui; Bollen, Mathieu; Shi, Yunyu

2009-01-01

Human FBP21 (formin-binding protein 21) contains a matrin-type zinc finger and two tandem WW domains. It is a component of the spliceosomes and interacts with several established splicing factors. Here we demonstrate for the first time that FBP21 is an activator of pre-mRNA splicing in vivo and that its splicing activation function and interaction with the splicing factor SIPP1 (splicing factor that interacts with PQBP1 and PP1) are both mediated by the two tandem WW domains of group III. We determined the solution structure of the tandem WW domains of FBP21 and found that the WW domains recognize peptide ligands containing either group II (PPLP) or group III (PPR) motifs. The binding interfaces involve both the XP and XP2 grooves of the two WW domains. Significantly, the tandem WW domains of FBP21 are connected by a highly flexible region, enabling their simultaneous interaction with two proline-rich motifs of SIPP1. The strong interaction between SIPP1 and FBP21 can be explained by the conjugation of two low affinity interactions with the tandem WW domains. Our study provides a structural basis for understanding the molecular mechanism underlying the functional implication of FBP21 and the biological specificity of tandem WW domains. PMID:19592703

Differential effects of THC- or CBD-rich cannabis extracts on working memory in rats.

PubMed

Fadda, Paola; Robinson, Lianne; Fratta, Walter; Pertwee, Roger G; Riedel, Gernot

2004-12-01

Cannabinoid receptors in the brain (CB(1)) take part in modulation of learning, and are particularly important for working and short-term memory. Here, we employed a delayed-matching-to-place (DMTP) task in the open-field water maze and examined the effects of cannabis plant extracts rich in either Delta(9)-tetrahydrocannabinol (Delta(9)-THC), or rich in cannabidiol (CBD), on spatial working and short-term memory formation in rats. Delta(9)-THC-rich extracts impaired performance in the memory trial (trial 2) of the DMTP task in a dose-dependent but delay-independent manner. Deficits appeared at doses of 2 or 5 mg/kg (i.p.) at both 30 s and 4 h delays and were similar in severity compared with synthetic Delta(9)-THC. Despite considerable amounts of Delta(9)-THC present, CBD-rich extracts had no effect on spatial working/short-term memory, even at doses of up to 50 mg/kg. When given concomitantly, CBD-rich extracts did not reverse memory deficits of the additional Delta(9)-THC-rich extract. CBD-rich extracts also did not alter Delta(9)-THC-rich extract-induced catalepsy as revealed by the bar test. It appears that spatial working/short-term memory is not sensitive to CBD-rich extracts and that potentiation and antagonism of Delta(9)-THC-induced spatial memory deficits is dependent on the ratio between CBD and Delta(9)-THC.

Application of Short Tandem Repeat markers in diagnosis of chromosomal aneuploidies and forensic DNA investigation in Pakistan.

PubMed

Chishti, Hafsah Muhammad; Ansar, Muhammad; Ajmal, Muhammad; Hameed, Abdul

2014-09-15

Short Tandem Repeat (STR) genetic markers hold great potential in forensic investigations, molecular diagnostics and molecular genetics research. AmpFlSTR® Identifiler™ PCR amplification kit is a multiplex system for co-amplification of 15 STR markers used worldwide in forensic investigations. This study attempts to assess forensic validity of these STRs in Pakistani population and to investigate its applicability in quick and simultaneous diagnosis and tracing parental source of common chromosomal aneuploidies. Samples from 554 healthy Pakistani individuals from 5 different ethnicities were analyzed for forensic parameters using Identifiler STRs and 74 patients' samples with different aneuploidies were evaluated for diagnostic strengths of these markers. All STRs hold sufficient forensic applicability in Pakistani population with paternity index between 1.5 and 3.5, polymorphic information content from 0.63 to 0.87 and discrimination power ≥0.9 (except TPOX locus). Variation from Hardy-Weinberg equilibrium was observed at some loci reflecting selective breeding and intermarriages trend in Pakistan. Among aneuploidic samples, all trisomies were precisely detectable while aneuploidies involving sex chromosomes or missing chromosomes were not clearly detectable using Identifiler STRs. Parental origin of aneuploidy was traceable in 92.54% patients. The studied STR markers are valuable tools for forensic application in Pakistan and utilizable for quick and simultaneous identification of some common trisomic conditions. Adding more sex chromosome specific STR markers can immensely increase the diagnostic and forensic potential of this system. Copyright © 2014 Elsevier B.V. All rights reserved.

Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization.

PubMed

Diegoli, Toni Marie; Rohde, Heinrich; Borowski, Stefan; Krawczak, Michael; Coble, Michael D; Nothnagel, Michael

2016-11-01

Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations. To meet the computational requirements of this family-based type of analysis, we modified a previous implementation so as to allow multi-core parallelization on a high-performance computing system. While we obtained recombination rate estimates larger than zero for all but one pair of adjacent markers within the four previously proposed linkage groups, none of the three X STR pairs defining the junctions of these groups yielded a recombination rate estimate of 0.50. Corroborating previous studies, our results therefore argue against a simple model of independent X chromosomal linkage groups. Moreover, the refined recombination fraction estimates obtained in our study will facilitate the appropriate joint consideration of all 15 investigated markers in forensic analysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Phytochemical analysis of Passiflora loefgrenii Vitta, a rich source of luteolin-derived flavonoids with antioxidant properties.

PubMed

Argentieri, Maria Pia; Levi, Marisa; Guzzo, Flavia; Avato, Pinarosa

2015-11-01

The paper describes the flavonoid composition of the aerial parts (young leaves, YL; adult leaves, AL; stems, ST) of Passiflora loefgrenii Vitta, a rare species native to Brazil, where it is traditionally used as food. Antioxidant potential has also been evaluated. To the best of our knowledge, no phytochemical and biological study on this species has been reported previously. Compositional data have been acquired combining HPLC-diode array detector (DAD) and Electrospary ionization-tandem mass spectrometry (ESI-MS/MS) analyses. Antioxidant activity has been evaluated by the 2,2'-di-phenyl-1-picrylhydrazyl method. Glycosylated flavones, with luteolin as the main aglycone, can be regarded as biomarkers for this drug. Qualitative composition of the extracts from YL, AL and ST was similar. The bulk of the constituents was made up by 8-C-ß-glucosyl luteolin (orientin), 7-O-α-rhamnosyl-6-C-ß-glucosyl luteolin and 6-C-α-rhamnosyl luteolin, which totally amounted to 16.57 (73%), 10.77 (74%) and 5.07 (77%) μg/mg in YL, AL and ST, respectively. P. loefgrenii showed a good antioxidant activity (IC50 of 350 μg/ml), higher than generally reported for other passifloras. P. loefgrenii, rich in luteolin glycosides, can be regarded as a good candidate to be explored for therapeutic properties other than the sedative one since it represents a rich source of valuable flavonoids with antioxidant potential. © 2015 Royal Pharmaceutical Society.

Comparison of Lateral Flow Assay, Kidney Inhibition Swab, and Liquid Chromatography-Tandem Mass Spectrometry for the Detection of Penicillin G Residues in Sow Urine.

PubMed

Shelver, Weilin L; Chakrabarty, Shubhashis; Smith, David J

2017-03-01

Sows (n = 126) were administered penicillin G; urine, collected at slaughter, was screened by kidney inhibition swab (KIS; 4 h testing time) and then stored at -80 °C (∼1200 days) until analysis by lateral flow assay (LF, ∼5 min testing time) and tandem quadrupole LC-MS/MS (TQ) analysis. The stability of penicillin in urine during storage was verified using TQ analyses. Quantitative results were well-correlated (R 2 = 0.98) with only a ∼10% decrease in penicillin concentration during the 3-year storage period. KIS retesting of stored samples returned results consistent with the original analyses. Lateral flow assay results were highly correlated with the KIS and TQ results. A KIS positive sample, which was not confirmed by TQ or LF, was assayed by Triple-TOF LC-MS to determine the cause of the apparent false positive. This study suggests LF can be used to quickly and efficiently screen for penicillin G residues before slaughter.

Coulomb repulsion in short polypeptides.

PubMed

Norouzy, Amir; Assaf, Khaleel I; Zhang, Shuai; Jacob, Maik H; Nau, Werner M

2015-01-08

Coulomb repulsion between like-charged side chains is presently viewed as a major force that impacts the biological activity of intrinsically disordered polypeptides (IDPs) by determining their spatial dimensions. We investigated short synthetic models of IDPs, purely composed of ionizable amino acid residues and therefore expected to display an extreme structural and dynamic response to pH variation. Two synergistic, custom-made, time-resolved fluorescence methods were applied in tandem to study the structure and dynamics of the acidic and basic hexapeptides Asp6, Glu6, Arg6, Lys6, and His6 between pH 1 and 12. (i) End-to-end distances were obtained from the short-distance Förster resonance energy transfer (sdFRET) from N-terminal 5-fluoro-l-tryptophan (FTrp) to C-terminal Dbo. (ii) End-to-end collision rates were obtained for the same peptides from the collision-induced fluorescence quenching (CIFQ) of Dbo by FTrp. Unexpectedly, the very high increase of charge density at elevated pH had no dynamical or conformational consequence in the anionic chains, neither in the absence nor in the presence of salt, in conflict with the common view and in partial conflict with accompanying molecular dynamics simulations. In contrast, the cationic peptides responded to ionization but with surprising patterns that mirrored the rich individual characteristics of each side chain type. The contrasting results had to be interpreted, by considering salt screening experiments, N-terminal acetylation, and simulations, in terms of an interplay of local dielectric constant and peptide-length dependent side chain charge-charge repulsion, side chain functional group solvation, N-terminal and side chain charge-charge repulsion, and side chain-side chain as well as side chain-backbone interactions. The common picture that emerged is that Coulomb repulsion between water-solvated side chains is efficiently quenched in short peptides as long as side chains are not in direct contact with each

Side chain-side chain interactions of arginine with tyrosine and aspartic acid in Arg/Gly/Tyr-rich domains within plant glycine-rich RNA binding proteins.

PubMed

Kumaki, Yasuhiro; Nitta, Katsutoshi; Hikichi, Kunio; Matsumoto, Takeshi; Matsushima, Norio

2004-07-01

Plant glycine-rich RNA-binding proteins (GRRBPs) contain a glycine-rich region at the C-terminus whose structure is quite unknown. The C-terminal glycine-rich part is interposed with arginine and tyrosine (arginine/glycine/tyrosine (RGY)-rich domain). Comparative sequence analysis of forty-one GRRBPs revealed that the RGY-rich domain contains multiple repeats of Tyr-(Xaa)h-(Arg)k-(Xaa)l, where Xaa is mainly Gly, "k" is 1 or 2, and "h" and "l" range from 0 to 10. Two peptides, 1 (G1G2Y3G4G5G6R7R8D9G10) and 2 (G1G2R3R4D5G6G7Y8G9G10), corresponding to sections of the RGY-rich domain in Zea mays RAB15, were selected for CD and NMR experiments. The CD spectra indicate a unique, positive band near 228 nm in both peptides that has been ascribed to tyrosine residues in ordered structures. The pH titration by NMR revealed that a side chain-side chain interaction, presumably an H-Nepsilon...O=Cgamma hydrogen bonding interaction in the salt bridge, occurs between Arg (i) and Asp (i + 2). 1D GOESY experiments indicated the presence of NOE between the aromatic side chain proton and the arginine side chain proton in the two peptides suggesting strongly that the Arg (i) aromatic side chain interacts directly with the Tyr (i +/- 4 or i +/- 5) side chain.

Ligand Binding to WW Tandem Domains of YAP2 Transcriptional Regulator Is Under Negative Cooperativity

PubMed Central

Schuchardt, Brett J.; Mikles, David C.; Hoang, Lawrence M.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

2014-01-01

YAP2 transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well-documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. PMID:25283809

Low-bandgap mixed tin–lead iodide perovskite absorbers with long carrier lifetimes for all-perovskite tandem solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Dewei; Yu, Yue; Wang, Changlei

Tandem solar cells using only metal-halide perovskite sub-cells are an attractive choice for next-generation solar cells. However, the progress in developing efficient all-perovskite tandem solar cells has been hindered by the lack of high-performance low-bandgap perovskite solar cells. Here in this paper, we report efficient mixed tin-lead iodide low-bandgap (~1.25 eV) perovskite solar cells with open-circuit voltages up to 0.85 V and over 70% external quantum efficiencies in the infrared wavelength range of 700-900 nm, delivering a short-circuit current density of over 29 mA cm -2 and demonstrating suitability for bottom-cell applications in all-perovskite tandem solar cells. Our low-bandgap perovskitemore » solar cells achieve a maximum power conversion efficiency of 17.6% and a certified efficiency of 17.01% with a negligible current-voltage hysteresis. Finally, when mechanically stacked with a ~1.58 eV bandgap perovskite top cell, our best all-perovskite 4-terminal tandem solar cell shows a steady-state efficiency of 21.0%.« less

Low-bandgap mixed tin–lead iodide perovskite absorbers with long carrier lifetimes for all-perovskite tandem solar cells

DOE PAGES

Zhao, Dewei; Yu, Yue; Wang, Changlei; ...

2017-03-01

Tandem solar cells using only metal-halide perovskite sub-cells are an attractive choice for next-generation solar cells. However, the progress in developing efficient all-perovskite tandem solar cells has been hindered by the lack of high-performance low-bandgap perovskite solar cells. Here in this paper, we report efficient mixed tin-lead iodide low-bandgap (~1.25 eV) perovskite solar cells with open-circuit voltages up to 0.85 V and over 70% external quantum efficiencies in the infrared wavelength range of 700-900 nm, delivering a short-circuit current density of over 29 mA cm -2 and demonstrating suitability for bottom-cell applications in all-perovskite tandem solar cells. Our low-bandgap perovskitemore » solar cells achieve a maximum power conversion efficiency of 17.6% and a certified efficiency of 17.01% with a negligible current-voltage hysteresis. Finally, when mechanically stacked with a ~1.58 eV bandgap perovskite top cell, our best all-perovskite 4-terminal tandem solar cell shows a steady-state efficiency of 21.0%.« less

Skewing of the genetic architecture at the ZMYM3 human-specific 5' UTR short tandem repeat in schizophrenia.

PubMed

Alizadeh, F; Bozorgmehr, A; Tavakkoly-Bazzaz, J; Ohadi, M

2018-06-01

Differential expansion of a number of human short tandem repeats (STRs) at the critical core promoter and 5' untranslated region (UTR) support the hypothesis that at least some of these STRs may provide a selective advantage in human evolution. Following a genome-wide screen of all human protein-coding gene 5' UTRs based on the Ensembl database ( http://www.ensembl.org ), we previously reported that the longest STR in this interval is a (GA) 32 , which belongs to the X-linked zinc finger MYM-type containing 3 (ZMYM3) gene. In the present study, we analyzed the evolutionary implication of this region across evolution and examined the allele and genotype distribution of the "exceptionally long" STR by direct sequencing of 486 Iranian unrelated male subjects consisting of 196 cases of schizophrenia (SCZ) and 290 controls. We found that the ZMYM3 transcript containing the STR is human-specific (ENST00000373998.5). A significant allele variance difference was observed between the cases and controls (Levene's test for equality of variances F = 4.00, p < 0.03). In addition, six alleles were observed in the SCZ patients that were not detected in the control group ("disease-only" alleles) (mid p exact < 0.0003). Those alleles were at the extreme short and long ends of the allele distribution curve and composed 4% of the genotypes in the SCZ group. In conclusion, we found skewing of the genetic architecture at the ZMYM3 STR in SCZ. Further, we found a bell-shaped distribution of alleles and selection against alleles at the extreme ends of this STR. The ZMYM3 STR sets a prototype, the evolutionary course of which determines the range of alleles in a particular species. Extreme "disease-only" alleles and genotypes may change our perspective of adaptive evolution and complex disorders. The ZMYM3 gene "exceptionally long" STR should be sequenced in SCZ and other human-specific phenotypes/characteristics.

Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.

PubMed

Nims, Raymond W; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera; Elmore, Eugene

2010-12-01

The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.

The thermal evolution of large water-rich asteroids

NASA Astrophysics Data System (ADS)

Schmidt, B. E.; Castillo, J. C.

2009-12-01

Water and heat played a significant role in the formation and evolution of large main belt asteroids, including 1 Ceres, 2 Pallas, and 24 Themis, for which there is now evidence of surficial water ice (Rivkin & Emery, ACM 2008). Shape measurements indicate some differentiation of Ceres’ interior, which, in combination with geophysical modeling, may indicate compositional layering in a core made up of anhydrous and hydrated silicate and a water ice mantle (Castillo-Rogez & McCord, in press, Icarus). We extend these interior models now to other large, possibly water-rich main belt asteroids, namely Pallas, at mean radius 272 km, and the Themis family parent body, at mean radius 150 km. The purpose of this study is to compare geophysical models against available constraints on the physical properties of these objects and to offer constraints on the origin of these objects. Pallas is the largest B-type asteroid. Its surface of hydrated minerals and recent constraint on its density, 2.4-2.8 g/cm3, seems to imply that water strongly affected its evolution (Schmidt et al., in press, Science). 24 Themis is the largest member of the Themis family that now counts about 580 members, including some of the main belt comets. The large member 90 Antiope has a density of about 1.2 g/cm3, while 24 Themis has a density of about 2.7 +/-1.3 g/cm3. The apparent contrast in the densities and spectral properties of the Themis family members may reflect a compositional layering in the original parent body. In the absence of tidal heating and with little accretional heat, the evolution of these small water-rich objects is a function of their initial composition and temperature. The latter depends on the location of formation (in the inner or outer solar system) and most importantly on the time and duration of accretion, which determines the amount of short-lived radioisotopes available for early internal activity. New accretional models suggest that planetesimals grew rapidly throughout

Authentic Assessment through Rich Tasks

ERIC Educational Resources Information Center

Wrigley, Terry

2017-01-01

This short article explains the key principles of "rich tasks," a version of authentic assessment developed in Queensland, Australia, as part of a major curriculum development called the "New Basics." In various documents, the project leaders recognised the danger that inappropriate assessment would undermine the proposed…

Broad-spectrum immunoaffinity cleanup for the determination of aflatoxins B1, B2, G1, G2, M1, M2 in Ophiocordyceps sinensis and its pharmaceutical preparations by ultra performance liquid chromatography tandem mass spectrometry.

PubMed

Sun, Shujuan; Xie, Jie; Peng, Tao; Shao, Bing; Zhu, Kui; Sun, Yuanze; Yao, Kai; Gu, Qiang; Zhang, Jing; Fan, Chunlin; Chen, Ying; Jiang, Haiyang

2017-11-15

An ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method was developed and validated for the simultaneous determination of aflatoxins B 1 , B 2 , G 1 , G 2 , M 1 and M 2 (AFB 1 , AFB 2 , AFG 1 , AFG 2 , AFM 1 and AFM 2 ) in Ophiocordyceps sinensis and its pharmaceutical preparations. A rapid and reliable immunoaffinity column containing a broad-spectrum monoclonal antibody for six aflatoxins was used for sample cleanup. Under the optimized conditions, the home-made immunoaffinity column capacity were about 315, 319, 292, 102, 444 and 369ng/mL gel for AFB 1 , AFB 2 , AFG 1 , AFG 2 , AFM 1 and AFM 2 , respectively. Recoveries for all tested aflatoxins ranged from 79.28% to 103.42% with relative standard deviation less than 8%. The limits of quantitation were in the range of 0.008-0.045μg/kg. Among 31 real samples analyzed, one sample was contaminated with AFB 1 , AFB 2 and AFM 1 at levels of 0.483, 0.068 and 0.104μg/kg, respectively. The established method is simple, accurate, and can be effectively used to determine the aflatoxins in Ophiocordyceps sinensis and its pharmaceutical preparations. Copyright © 2017 Elsevier B.V. All rights reserved.

The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

PubMed

Zou, Zheng-Ting; Uphyrkina, Olga V; Fomenko, Pavel; Luo, Shu-Jin

2015-07-01

Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Two different size classes of 5S rDNA units coexisting in the same tandem array in the razor clam Ensis macha: is this region suitable for phylogeographic studies?

PubMed

Fernández-Tajes, Juan; Méndez, Josefina

2009-12-01

For a study of 5S ribosomal genes (rDNA) in the razor clam Ensis macha, the 5S rDNA region was amplified and sequenced. Two variants, so-called type I or short repeat (approximately 430 bp) and type II or long repeat (approximately 735 bp), appeared to be the main components of the 5S rDNA of this species. Their spacers differed markedly, both in length and nucleotide composition. The organization of the two variants was investigated by amplifying the genomic DNA with primers based on the sequence of the type I and type II spacers. PCR amplification products with primers EMLbF and EMSbR showed that the long and short repeats are associated within the same tandem array, suggesting an intermixed arrangement of both spacers. Nevertheless, amplifications carried out with inverse primers EMSinvF/R and EMLinvF/R revealed that some short and long repeats are contiguous in the same tandem array. This is the first report of the coexistence of two variable spacers in the same tandem array in bivalve mollusks.

A missing population of short duration gamma-ray bursts

NASA Astrophysics Data System (ADS)

Troja, Eleonora

Short duration gamma-ray bursts (GRBs) are brief and intense flashes of gamma-ray radiation located at cosmological distances. NASA s Swift mission provided the first breakthrough observations connecting these high-energy transients to the coalescence of two compact objects, either two neutron stars (NSs) or a NS and a black hole (BH). Short GRBs are therefore prime candidate electromagnetic counterparts of gravitational wave sources detectable by advanced LIGO. Unfortunately, only a fraction of short GRBs visible by Swift is promptly identified by the on-board trigger system. A larger number of events fails to pass the on-board trigger selection and goes unnoticed. Luckily, this subset of events is not lost. It is instead downlinked through a low-priority channel and then archived. The goal of this ADAP proposal is to harvest this rich population of gamma-ray transients buried in the data archive. We propose to 1) systematically mine this untapped resource of the Swift archive in order to discover new short GRBs; 2) correlate the Swift untriggered dataset with signals detected by other facilities (e.g Fermi, INTEGRAL), at other wavelengths (e.g. fast radio bursts) or with other messengers (e.g. gravitational waves); 3) develop and release the relevant tools and documentation to the community in order to facilitate the exploitation of this valuable dataset in future years. The proposed research will significantly expand the current database of short GRBs, and aid multimessenger searches of transient phenomena. By studying the behavior of matter in extreme physical conditions, the formation of new black holes, and gravity, this project directly addresses NASA Strategic Objective 1.6, a key science goal in the area of Cosmic Origins.

Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.

PubMed

Rajagopal, J; Das, S; Khurana, D K; Srivastava, P S; Lakshmikumaran, M

1999-10-01

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012

PubMed Central

Oberacher, Herbert

2013-01-01

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification. PMID:24957994

Tandem Organic Light-Emitting Diodes.

PubMed

Fung, Man-Keung; Li, Yan-Qing; Liao, Liang-Sheng

2016-12-01

A tandem organic light-emitting diode (OLED) is an organic optoelectronic device that has two or more electroluminescence (EL) units connected electrically in series with unique intermediate connectors within the device. Researchers have studied this new OLED architecture with growing interest and have found that the current efficiency of a tandem OLED containing N EL units (N > 1) should be N times that of a conventional OLED containing only a single EL unit. Therefore, this new architecture is potentially useful for constructing high-efficiency, high-luminance, and long-lifetime OLED displays and organic solid-state lighting sources. In a tandem OLED, the intermediate connector plays a crucial role in determining the effectiveness of the stacked EL units. The interfaces in the connector control the inner charge generation and charge injection into the adjacent EL units. Meanwhile, the transparency and the thickness of the connector affect the light output of the device. Therefore, the intermediate connector should be made to meet both the electrical and optical requirements for achieving optimal performance. Here, recent advances in the research of the tandem OLEDs is discussed, with the main focus on material selection and interface studies in the intermediate connectors, as well as the optical design of the tandem OLEDs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

PubMed

Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

2014-12-01

YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. © 2014 FEBS.

Anthocyanin-Rich Grape Pomace Extract (Vitis vinifera L.) from Wine Industry Affects Mitochondrial Bioenergetics and Glucose Metabolism in Human Hepatocarcinoma HepG2 Cells.

PubMed

de Sales, Nathalia F F; Silva da Costa, Leandro; Carneiro, Talita I A; Minuzzo, Daniela A; Oliveira, Felipe L; Cabral, Lourdes M C; Torres, Alexandre G; El-Bacha, Tatiana

2018-03-08

Cancer cells demand high ATP provisions to support proliferation, and targeting of energy metabolism is a good strategy to increase their sensitivity to treatments. In Brazil, wine manufacture is expanding, increasing the amount of pomace that is produced. We determined the phenolic composition and antioxidant properties of a dark skin Grape Pomace Extract and its effects on metabolism and redox state in human hepatocarcinoma HepG2 cells. The material and the methods used represented the industrial process since pomace derived from white wine production and the extract concentrated by pilot plant scale reverse osmosis. Grape pomace extract was rich in polyphenols, mainly anthocyanins, and presented high antioxidant capacity. Short-term metabolic effects, irrespective of any cytotoxicity, involved increased mitochondrial respiration and antioxidant capacity and decreased glycolytic metabolism. Long-term incubation was cytotoxic and cells died by necrosis and GPE was not toxic to non-cancer human fibroblasts. To the best of our knowledge, this is the first report to characterize pomace extract from white wine production from Brazilian winemaking regarding its effects on energy metabolism, suggesting its potential use for pharmaceutical and nutraceutical purposes.

G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structures in vitro and are unwound by the Pfh1 DNA helicase

PubMed Central

Wallgren, Marcus; Mohammad, Jani B.; Yan, Kok-Phen; Pourbozorgi-Langroudi, Parham; Ebrahimi, Mahsa; Sabouri, Nasim

2016-01-01

Certain guanine-rich sequences have an inherent propensity to form G-quadruplex (G4) structures. G4 structures are e.g. involved in telomere protection and gene regulation. However, they also constitute obstacles during replication if they remain unresolved. To overcome these threats to genome integrity, organisms harbor specialized G4 unwinding helicases. In Schizosaccharomyces pombe, one such candidate helicase is Pfh1, an evolutionarily conserved Pif1 homolog. Here, we addressed whether putative G4 sequences in S. pombe can adopt G4 structures and, if so, whether Pfh1 can resolve them. We tested two G4 sequences, derived from S. pombe ribosomal and telomeric DNA regions, and demonstrated that they form inter- and intramolecular G4 structures, respectively. Also, Pfh1 was enriched in vivo at the ribosomal G4 DNA and telomeric sites. The nuclear isoform of Pfh1 (nPfh1) unwound both types of structure, and although the G4-stabilizing compound Phen-DC3 significantly enhanced their stability, nPfh1 still resolved them efficiently. However, stable G4 structures significantly inhibited adenosine triphosphate hydrolysis by nPfh1. Because ribosomal and telomeric DNA contain putative G4 regions conserved from yeasts to humans, our studies support the important role of G4 structure formation in these regions and provide further evidence for a conserved role for Pif1 helicases in resolving G4 structures. PMID:27185885

Randomized trial of oral misoprostol treatment for cervical ripening before tandem application in cervix cancer.

PubMed

Cepni, Kimia; Gul, Sule; Cepni, Ismail; Güralp, Onur; Sal, Veysel; Mayadagli, Alpaslan

2011-11-01

To investigate the efficacy of oral misoprostol administered to facilitate tandem application to the cervix as a part of brachytherapy in patients with cervical cancer. Eighty patients with cervical cancer who had been planned to undergo brachytherapy at Dr. Lütfi Kırdar Kartal Training and Research Hospital were evaluated in a double-blind, prospective, randomized trial. Patients were divided randomly into two groups of 40 patients. The first and second groups received 400 μg of misoprostol orally and placebo, respectively, 3 h before tandem application. The two groups were compared in terms of age, diameter of tumor, parity, age at first intercourse, amount of bleeding and pain at first tandem application, length of endometrial cavity measured by hysterometer, and size of Hegar dilators used for cervical dilatation. Of all cases, 63.6%, 16.3%, 10%, 6.3%, 2.5%, and 1.3% were Stage IIB, IIIB, IIIA, IVA, IIA and IIC, respectively. Mean (±SD) age (range) was 49.3 ± 13.1 (25-83) years and 56.6 ± 13.2 (30-78) years in the study and control groups, respectively (p = 0.015). Age at first intercourse, diameter of tumor, parity, amount of bleeding at first tandem application, and length of endometrial cavity measured by hysterometer were not significantly different between the two groups. Pain score was significantly higher in the control group (p < 0.001). Application was significantly easier in the study group compared with controls (p < 0.001). Average size of initial Hegar dilators used for cervical dilatation was significantly higher in the study group compared with controls (p = 0.017). Administration of misoprostol 400 μg orally for cervical ripening before tandem application facilitates the procedure, increases patient tolerability and comfort, and may decrease complication rates. Copyright © 2011 Elsevier Inc. All rights reserved.

Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oetting, W.S.; Lee, H.K.; Flanders, D.J.

The use of short tandem repeat polymorphisms (STRPs) as marker loci for linkage analysis is becoming increasingly important due to their large numbers in the human genome and their high degree of polymorphism. Fluorescence-based detection of the STRP pattern with an automated DNA sequencer has improved the efficiency of this technique by eliminating the need for radioactivity and producing a digitized autoradiogram-like image that can be used for computer analysis. In an effort to simplify the procedure and to reduce the cost of fluorescence STRP analysis, we have developed a technique known as multiplexing STRPs with tailed primers (MSTP) usingmore » primers that have a 19-bp extension, identical to the sequence of an M13 sequencing primer, on the 5{prime} end of the forward primer in conjunction with multiplexing several primer pairs in a single polymerase chain reaction (PCR) amplification. The banding pattern is detected with the addition of the M13 primer-dye conjugate as the sole primer conjugated to the fluorescent dye, eliminating the need for direct conjugation of the infrared fluorescent dye to the STRP primers. The use of MSTP for linkage analysis greatly reduces the number of PCR reactions. Up to five primer pairs can be multiplexed together in the same reaction. At present, a set of 148 STRP markers spaced at an average genetic distance of 28 cM throughout the autosomal genome can be analyzed in 37 sets of multiplexed amplification reactions. We have automated the analysis of these patterns for linkage using software that both detects the STRP banding pattern and determines their sizes. This information can then be exported in a user-defined format from a database manager for linkage analysis. 15 refs., 2 figs., 4 tabs.« less

High voltage series connected tandem junction solar battery

DOEpatents

Hanak, Joseph J.

1982-01-01

A high voltage series connected tandem junction solar battery which comprises a plurality of strips of tandem junction solar cells of hydrogenated amorphous silicon having one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon, arranged in a tandem configuration, can have the same bandgap or differing bandgaps. The tandem junction strip solar cells are series connected to produce a solar battery of any desired voltage.

Tandem Solar Cells from Accessible Low Band-Gap Polymers Using an Efficient Interconnecting Layer.

PubMed

Bag, Santanu; Patel, Romesh J; Bunha, Ajaykumar; Grand, Caroline; Berrigan, J Daniel; Dalton, Matthew J; Leever, Benjamin J; Reynolds, John R; Durstock, Michael F

2016-01-13

Tandem solar cell architectures are designed to improve device photoresponse by enabling the capture of wider range of solar spectrum as compared to single-junction device. However, the practical realization of this concept in bulk-heterojunction polymer systems requires the judicious design of a transparent interconnecting layer compatible with both polymers. Moreover, the polymers selected should be readily synthesized at large scale (>1 kg) and high performance. In this work, we demonstrate a novel tandem polymer solar cell that combines low band gap poly isoindigo [P(T3-iI)-2], which is easily synthesized in kilogram quantities, with a novel Cr/MoO3 interconnecting layer. Cr/MoO3 is shown to be greater than 80% transparent above 375 nm and an efficient interconnecting layer for P(T3-iI)-2 and PCDTBT, leading to 6% power conversion efficiencies under AM 1.5G illumination. These results serve to extend the range of interconnecting layer materials for tandem cell fabrication by establishing, for the first time, that a thin, evaporated layer of Cr/MoO3 can work as an effective interconnecting layer in a tandem polymer solar cells made with scalable photoactive materials.

Educational activities with a tandem accelerator

NASA Astrophysics Data System (ADS)

Casolaro, P.; Campajola, L.; Balzano, E.; D'Ambrosio, E.; Figari, R.; Vardaci, E.; La Rana, G.

2018-05-01

Selected experiments in fundamental physics have been proposed for many years at the Tandem Accelerator of the University of Napoli ‘Federico II’s Department of Physics as a part of a one-semester laboratory course for graduate students. The aim of this paper is to highlight the educational value of the experimental realization of the nuclear reaction 19F(p,α)16O. With the purpose of verifying the mass-energy equivalence principle, different aspects of both classical and modern physics can be investigated, e.g. conservation laws, atomic models, nuclear physics applications to compositional analysis, nuclear cross-section, Q-value and nuclear spectroscopic analysis.

[Polymorphism analysis of 20 autosomal short-tandem repeat loci in southern Chinese Han population].

PubMed

Chen, Ling; Lu, Hui-Jie; DU, Wei-An; Qiu, Ping-Ming; Liu, Chao

2016-02-20

To evaluate the value of PowerPlex ® 21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population. We conducted genotyping experiments using PowerPlex ® 21 System on 20 autosomal STR loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations. The PowerPlex ® 21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China. The 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases

PubMed Central

Feschenko, Vladimir V.; Rajman, Luis A.; Lovett, Susan T.

2003-01-01

Rearrangements between tandemly repeated DNA sequences are a common source of genetic instability. Such rearrangements underlie several human genetic diseases. In many organisms, the mismatch-repair (MMR) system functions to stabilize repeats when the repeat unit is short or when sequence imperfections are present between the repeats. We show here that the action of single-stranded DNA (ssDNA) exonucleases plays an additional, important role in stabilizing tandem repeats, independent of their role in MMR. For perfect repeats of ≈100 bp in Escherichia coli that are not susceptible to MMR, exonuclease (Exo)-I, ExoX, and RecJ exonuclease redundantly inhibit deletion. Our data suggest that >90% of potential deletion events are avoided by the combined action of these three exonucleases. Imperfect tandem repeats, less prone to rearrangements, are stabilized by both the MMR-pathway and ssDNA-specific exonucleases. For 100-bp repeats containing four mispairs, ExoI alone aborts most deletion events, even in the presence of a functional MMR system. By genetic analysis, we show that the inhibitory effect of ssDNA exonucleases on deletion formation is independent of the MutS and UvrD proteins. Exonuclease degradation of DNA displaced during the deletion process may abort slipped misalignment. Exonuclease action is therefore a significant force in genetic stabilization of many forms of repetitive DNA. PMID:12538867

CdCl2 passivation of polycrystalline CdMgTe and CdZnTe absorbers for tandem photovoltaic cells

NASA Astrophysics Data System (ADS)

Swanson, Drew E.; Reich, Carey; Abbas, Ali; Shimpi, Tushar; Liu, Hanxiao; Ponce, Fernando A.; Walls, John M.; Zhang, Yong-Hang; Metzger, Wyatt K.; Sampath, W. S.; Holman, Zachary C.

2018-05-01

As single-junction silicon solar cells approach their theoretical limits, tandems provide the primary path to higher efficiencies. CdTe alloys can be tuned with magnesium (CdMgTe) or zinc (CdZnTe) for ideal tandem pairing with silicon. A II-VI/Si tandem holds the greatest promise for inexpensive, high-efficiency top cells that can be quickly deployed in the market using existing polycrystalline CdTe manufacturing lines combined with mature silicon production lines. Currently, all high efficiency polycrystalline CdTe cells require a chloride-based passivation process to passivate grain boundaries and bulk defects. This research examines the rich chemistry and physics that has historically limited performance when extending Cl treatments to polycrystalline 1.7-eV CdMgTe and CdZnTe absorbers. A combination of transmittance, quantum efficiency, photoluminescence, transmission electron microscopy, and energy-dispersive X-ray spectroscopy clearly reveals that during passivation, Mg segregates and out-diffuses, initially at the grain boundaries but eventually throughout the bulk. CdZnTe exhibits similar Zn segregation behavior; however, the onset and progression is localized to the back of the device. After passivation, CdMgTe and CdZnTe can render a layer that is reduced to predominantly CdTe electro-optical behavior. Contact instabilities caused by inter-diffusion between the layers create additional complications. The results outline critical issues and paths for these materials to be successfully implemented in Si-based tandems and other applications.

CdCl2 Passivation of Polycrystalline CdMgTe and CdZnTe Absorbers for Tandem Photovoltaic Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metzger, Wyatt K; Swanson, Drew; Reich, Carey

As single-junction silicon solar cells approach their theoretical limits, tandems provide the primary path to higher efficiencies. CdTe alloys can be tuned with magnesium (CdMgTe) or zinc (CdZnTe) for ideal tandem pairing with silicon. A II-VI/Si tandem holds the greatest promise for inexpensive, high-efficiency top cells that can be quickly deployed in the market using existing polycrystalline CdTe manufacturing lines combined with mature silicon production lines. Currently, all high efficiency polycrystalline CdTe cells require a chloride-based passivation process to passivate grain boundaries and bulk defects. This research examines the rich chemistry and physics that has historically limited performance when extendingmore » Cl treatments to polycrystalline 1.7-eV CdMgTe and CdZnTe absorbers. A combination of transmittance, quantum efficiency, photoluminescence, transmission electron microscopy, and energy-dispersive X-ray spectroscopy clearly reveals that during passivation, Mg segregates and out-diffuses, initially at the grain boundaries but eventually throughout the bulk. CdZnTe exhibits similar Zn segregation behavior; however, the onset and progression is localized to the back of the device. After passivation, CdMgTe and CdZnTe can render a layer that is reduced to predominantly CdTe electro-optical behavior. Contact instabilities caused by inter-diffusion between the layers create additional complications. The results outline critical issues and paths for these materials to be successfully implemented in Si-based tandems and other applications.« less

Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques

NASA Astrophysics Data System (ADS)

Benito, S.; Ferrer, A.; Benabou, S.; Aviñó, A.; Eritja, R.; Gargallo, R.

2018-05-01

Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 105 M-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.

Production of conjugated linoleic acid-rich potato chips.

PubMed

Jain, Vishal P; Proctor, Andrew

2007-01-01

Conjugated linoleic acid (CLA) is found primarily in diary and beef products, but the health benefits of CLA can only be realized if they are consumed at much greater levels than a normal healthy dietary intake. We have recently shown that a CLA-rich soy oil can be produced by simple isomerization of linoleic acid in soy oil by photoirradiation. This oil may allow greatly increased dietary CLA without significantly elevating fat intake. The objective of this study was to prepare CLA-rich potato chips by frying in CLA-rich soy oil. Soy oil was photoisomerized in the presence of iodine catalyst with UV/visible light. The irradiated oil was clay processed to remove the residual iodine and this oil was then used to fry potato chips. Oil was extracted from fried chips and analyzed for its CLA content with gas chromatography. A 1-oz serving of CLA-rich potato chips contained approximately 2.4 g CLA as compared to 0.1 g CLA in 3-oz serving of steak fillet and 0.06 g CLA in 8-oz serving of whole milk. The peroxide value of the oil extracted from potato chips was found to be 1 meq/1000 g sample, which was within the acceptable commercial standards. This study may lead to the commercialization of CLA-rich food products.

Development of High Efficiency Four-Terminal Perovskite-Silicon Tandems

NASA Astrophysics Data System (ADS)

Duong, The Duc

the films. Rb-doping is studied under different excess PbI2 concentrations and the optimal condition is found to be 5% Rb-doping and 15% excess PbI2 concentration. The addition of more than 10% Rb results in the formation of an unwanted Rb-rich phase due to the significant lattice mismatch between Rb and FA/MA cations. An efficiency of 18.8% is achieved for the champion cell as compared to 16% with control cells. Importantly, Rb-doping improves the light, moisture and thermal stability of perovskite cells. The optimal bandgap of the perovskite top cell in perovskite-silicon tandems is between 1.7 eV and 1.8 eV. A quadruple-cation Rb/Cs/FA/MA mixed-halide I/Br perovskite composition is explored to obtain high quality perovskite films with a bandgap of 1.73 eV. The ratio between Cs/FA/MA cations is critical to the morphology, crystal orientation and electronic properties of perovskite films. Furthermore, 5% Rb-doping enhances the crystallinity and suppresses defect migration in the films. Semi-transparent cells with efficiencies up to 16% and negligible hysteresis are achieved using this material. With excellent transparency and optimal bandgap of the semi-transparent perovskite cell, a record four-terminal mechanically stacked perovskite-silicon tandem efficiency of 26.4% is achieved.

Genetic variation in a compound short tandem repeat/Alu haplotype system at the SB19.3 locus: properties and interpretation.

PubMed

Gaspar, Paulo; Seixas, Susana; Rocha, Jorge

2004-04-01

The genetic variation at a compound nonrecombining haplotype system, consisting of the previously reported SB19.3 Alu insertion polymorphism and a newly identified adjacent short tandem repeat (STR), was studied in population samples from Portugal and São Tomé (Gulf of Guinea, West Africa). Age estimates based on the linked microsatellite variation suggest that the Alu insertion occurred about 190,000 years ago. In accordance with the global patterns of distribution of human genetic variation, the highest haplotype diversity was found in the African sample. This excess in African diversity was due to both a substantial reduction in heterozygosity at the Alu polymorphism and a lower STR variability associated with the predominant Alu insertion allele in the Portuguese sample. The high level of interpopulation differentiation observed at the Alu locus (F(ST) = 0.43) was interpreted under alternative selective and demographic scenarios. The need for compatibility between patterns of variation at the STR and Alu loci could be used to restrict the range of selection coefficients in selection-driven genetic hitchhiking frameworks and to favor demographic scenarios dominated by larger pre-expansion African population sizes. Taken together, the data show that the SB19.3 Alu-STR system is an informative marker that can be included in more extended batteries of compound haplotypes used in human evolutionary studies.

Identification of exhumed remains of fire tragedy victims using conventional methods and autosomal/Y-chromosomal short tandem repeat DNA profiling.

PubMed

Calacal, Gayvelline C; Delfin, Frederick C; Tan, Michelle Music M; Roewer, Lutz; Magtanong, Danilo L; Lara, Myra C; Fortun, Raquel dR; De Ungria, Maria Corazon A

2005-09-01

In a fire tragedy in Manila in December 1998, one of the worst tragic incidents which resulted in the reported death of 23 children, identity could not be established initially resulting in the burial of still unidentified bodies. Underscoring the importance of identifying each of the human remains, the bodies were exhumed 3 months after the tragedy. We describe here our work, which was the first national case handled by local laboratories wherein conventional and molecular-based techniques were successfully applied in forensic identification. The study reports analysis of DNA obtained from skeletal remains exposed to conditions of burning, burial, and exhumation. DNA typing methods using autosomal and Y-chromosomal short tandem repeat (Y-STR) markers reinforced postmortem examinations using conventional identification techniques. The strategy resulted in the identification of 18 out of the 21 human remains analyzed, overcoming challenges encountered due to the absence of established procedures for the recovery of mass disaster remains. There was incomplete antemortem information to match the postmortem data obtained from the remains of 3 female child victims. Two victims were readily identified due to the availability of antemortem tissues. In the absence of this biologic material, parentage testing was performed using reference blood samples collected from parents and relatives. Data on patrilineal lineage based on common Y-STR haplotypes augmented autosomal DNA typing, particularly in deficiency cases.

Genetic considerations in human sex-mate selection: partners share human leukocyte antigen but not short-tandem-repeat identity markers.

PubMed

Israeli, Moshe; Kristt, Don; Nardi, Yuval; Klein, Tirza

2014-05-01

Previous studies support a role for MHC on mating preference, yet it remains unsettled as to whether mating occurs preferentially between individuals sharing human leukocyte antigen (HLA) determinants or not. Investigating sex-mate preferences in the contemporary Israeli population is of further curiosity being a population with distinct genetic characteristics, where multifaceted cultural considerations influence mate selection. Pairs of male-female sex partners were evaluated in three groups. Two groups represented unmarried (n = 1002) or married (n = 308) couples and a control group of fictitious male-female couples. HLA and short-tandem-repeat (STR) genetic identification markers were assessed for the frequency of shared antigens and alleles. Human leukocyte antigen results showed that Class I and/ or Class II single antigen as well as double antigen sharing was more common in sex partners than in control group couples (P < 0.001). Married versus unmarried pairs were not distinguishable. In contrast, STR-DNA markers failed to differentiate between sex-mates and controls (P = 0.78). Sex partnerships shared HLA determinants more frequently than randomly constituted male-female pairs. The observed phenomenon does not reflect a syngenetic background between sex-mates as STR markers were not selectively shared. Thus, sex-mate selection in man may contravene the evolutionary pressure for genetic diversity in regard to HLA. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria.

PubMed Central

Vioque, A

1997-01-01

The RNase P RNA gene (rnpB) from 10 cyanobacteria has been characterized. These new RNAs, together with the previously available ones, provide a comprehensive data set of RNase P RNA from diverse cyanobacterial lineages. All heterocystous cyanobacteria, but none of the non-heterocystous strains analyzed, contain short tandemly repeated repetitive (STRR) sequences that increase the length of helix P12. Site-directed mutagenesis experiments indicate that the STRR sequences are not required for catalytic activity in vitro. STRR sequences seem to have recently and independently invaded the RNase P RNA genes in heterocyst-forming cyanobacteria because closely related strains contain unrelated STRR sequences. Most cyanobacteria RNase P RNAs lack the sequence GGU in the loop connecting helices P15 and P16 that has been established to interact with the 3'-end CCA in precursor tRNA substrates in other bacteria. This character is shared with plastid RNase P RNA. Helix P6 is longer than usual in most cyanobacteria as well as in plastid RNase P RNA. PMID:9254706

Hydrodynamic studies on two traveling wavy foils in tandem arrangement

NASA Astrophysics Data System (ADS)

Deng, Jian; Shao, Xue-Ming; Yu, Zhao-Sheng

2007-11-01

In this study, the hydrodynamic interactions between two tandem foils undergoing fishlike swimming motion are investigated numerically by solving the Navier-Stokes equations with the immersed-boundary method. The two foils represent two tandem propellers attached on a concept ship. The thrusts and efficiencies at three typical Strouhal numbers, i.e., St =0.4, 0.6, and 0.8, are investigated. The results show that a fish situated directly behind another one does not always undergo a lower thrust. Whether it experiences a thrust enhancement or reduction depends on the Strouhal number. At a relatively low Strouhal number (e.g., St =0.4), the usual wake drag-reduction effect predominates over the drag-enhancement effect caused by the reverse von Kármán vortices, resulting in a thrust enhancement. The opposite happens at a relatively high Strouhal number (e.g., St =0.8). The downstream fish can benefit from the upstream one by slalom between the vortices rather than through them. For the upstream fish, the thrusts and efficiencies for all Strouhal numbers studied are higher than those for a single fish when the two fish are closely spaced, and approach those for a single fish as the spacing is increased.

Structure revision of hupehensis saponin F and G and characterization of new trace triterpenoid saponins from Anemone hupehensis by tandem electrospray ionization mass spectrometry.

PubMed

Li, Fu; Liu, Xin; Tang, Minghai; Chen, Bin; Ding, Lisheng; Chen, Lijuan; Wang, Mingkui

2012-05-15

Electrospray ionization ion-trap tandem mass spectrometry (ESI-MS(n)) was first employed for reinvestigating the structures of hupehensis saponin F and G previously isolated from Anemone hupehensis in our lab. Hupehensis saponin G was determined to contain one more trisaccharide unit (Rha-(1→4)-Glc-(1→6)-Glc-), not a glucose residue, than saponin F based on their molecular weights deduced from their [M+Na](+) ions in ESI-MS spectra. The (2,4)A(4α)-ion at m/z 551.3 formed by retro-Diels-Alder (RDA) rearrangement in positive mode illustrated that the C-28 sugar chains of the two saponins were composed of trisaccharide repeating moieties with (1→4) linkages rather than (1→3) linkages. The interpretation of 2D-NMR spectra of the two compounds also confirmed the results obtained by ESI-MS(n). Moreover, from the water soluble part of A. hupehensis, two novel triterpene saponins were tentatively characterized to contain 4 and 5 (1→4)-linked above trisaccharide repeating moieties at C-28 position according to their ESI-MS(n) behaviors, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Tandem Translation Classroom: A Case Study

ERIC Educational Resources Information Center

Kim, Dohun; Koh, Taejin

2018-01-01

The transition to student-centred learning, advances in teleconferencing tools, and active international student exchange programmes have stimulated tandem learning in many parts of the world. This pedagogical model is based on a mutual language exchange between tandem partners, where each student is a native speaker in the language the…

Fast quantitative detection of cocaine in beverages using nanoextractive electrospray ionization tandem mass spectrometry.

PubMed

Hu, Bin; Peng, Xuejiao; Yang, Shuiping; Gu, Haiwei; Chen, Huanwen; Huan, Yanfu; Zhang, Tingting; Qiao, Xiaolin

2010-02-01

Without any sample pretreatment, effervescent beverage fluids were manually sprayed into the primary ion plume created by using a nanoelectrospray ionization source for direct ionization, and the analyte ions of interest were guided into an ion trap mass spectrometer for tandem mass analysis. Functional ingredients (e.g., vitamins, taurine, and caffeine, etc.) and spiked impurity (e.g., cocaine) in various beverages, such as Red Bull energy drink, Coco-cola, and Pepsi samples were rapidly identified within 1.5 s. The limit of detection was found to be 7-15 fg (S/N = 3) for cocaine in different samples using the characteristic fragment (m/z 150) observed in the MS(3) experiments. Typical relative standard deviation and recovery of this method were 6.9%-8.6% and 104%-108% for direct analysis of three actual samples, showing that nanoextractive electrospray ionization tandem mass spectrometry is a useful technique for fast screening cocaine presence in beverages. 2010. Published by Elsevier Inc.

UV-Vis Action Spectroscopy Reveals a Conformational Collapse in Hydrogen-Rich Dinucleotide Cation Radicals.

PubMed

Korn, Joseph A; Urban, Jan; Dang, Andy; Nguyen, Huong T H; Tureček, František

2017-09-07

We report the generation of deoxyriboadenosine dinucleotide cation radicals by gas-phase electron transfer to dinucleotide dications and their noncovalent complexes with crown ether ligands. Stable dinucleotide cation radicals of a novel hydrogen-rich type were generated and characterized by tandem mass spectrometry and UV-vis photodissociation (UVPD) action spectroscopy. Electron structure theory analysis indicated that upon electron attachment the dinucleotide dications underwent a conformational collapse followed by intramolecular proton migrations between the nucleobases to give species whose calculated UV-vis absorption spectra matched the UVPD action spectra. Hydrogen-rich cation radicals generated from chimeric riboadenosine 5'-diesters gave UVPD action spectra that pointed to novel zwitterionic structures consisting of aromatic π-electron anion radicals intercalated between stacked positively charged adenine rings. Analogies with DNA ionization are discussed.

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

PubMed Central

Christiansen, Martha E.; Znosko, Brent M.

2009-01-01

Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329–4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence. PMID:19509311

Selecting tandem partners for silicon solar cells [Selecting tandem partners for silicon solar cells using spectral efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Zhengshan; Leilaeioun, Mehdi; Holman, Zachary

Combining silicon and other materials in tandem solar cells is one approach to enhancing the overall power conversion efficiency of the cells. Here, we argue that top cell partners for silicon tandem solar cells should be selected on the basis of their spectral efficiency — their efficiency resolved by wavelength.

Selecting tandem partners for silicon solar cells [Selecting tandem partners for silicon solar cells using spectral efficiency

DOE PAGES

Yu, Zhengshan; Leilaeioun, Mehdi; Holman, Zachary

2016-09-26

Combining silicon and other materials in tandem solar cells is one approach to enhancing the overall power conversion efficiency of the cells. Here, we argue that top cell partners for silicon tandem solar cells should be selected on the basis of their spectral efficiency — their efficiency resolved by wavelength.

Tandem junction amorphous silicon solar cells

DOEpatents

Hanak, Joseph J.

1981-01-01

An amorphous silicon solar cell has an active body with two or a series of layers of hydrogenated amorphous silicon arranged in a tandem stacked configuration with one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon arranged in tandem configuration can have the same bandgap or differing bandgaps.

Anaerobic co-digestion of acetate-rich with lignin-rich wastewater and the effect of hydrotalcite addition.

PubMed

Rodriguez-Chiang, Lourdes; Llorca, Jordi; Dahl, Olli

2016-10-01

The methane potential and biodegradability of different ratios of acetate and lignin-rich effluents from a neutral sulfite semi-chemical (NSSC) pulp mill were investigated. Results showed ultimate methane yields up to 333±5mLCH4/gCOD when only acetate-rich substrate was added and subsequently lower methane potentials of 192±4mLCH4/gCOD when the lignin fraction was increased. The presence of lignin showed a linear decay in methane production, resulting in a 41% decrease in methane when the lignin-rich feed had a 30% increase. A negative linear correlation between lignin content and biodegradability was also observed. Furthermore, the effect of hydrotalcite (HT) addition was evaluated and showed increase in methane potential of up to 8%, a faster production rate and higher soluble lignin removal (7-12% higher). Chemical oxygen demand (COD) removal efficiencies between 64 and 83% were obtained for all samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA

PubMed Central

Munroe, Stephen H.; Morales, Christopher H.; Duyck, Tessa H.; Waters, Paul D.

2015-01-01

The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3’ end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3’splice site of TRα2 mRNA and antisense to the 3’UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing. PMID:26368571

Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.

PubMed

Liu, San-Xu; Hou, Wei; Zhang, Xue-Yan; Peng, Chang-Jun; Yue, Bi-Song; Fan, Zhen-Xin; Li, Jing

2018-07-18

The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (P<0.05, t-test). We also found a greater number of homozygous STRs than heterozygous STRs (P<0.05, t-test), with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations. The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for

High-Efficiency Polycrystalline Thin Film Tandem Solar Cells.

PubMed

Kranz, Lukas; Abate, Antonio; Feurer, Thomas; Fu, Fan; Avancini, Enrico; Löckinger, Johannes; Reinhard, Patrick; Zakeeruddin, Shaik M; Grätzel, Michael; Buecheler, Stephan; Tiwari, Ayodhya N

2015-07-16

A promising way to enhance the efficiency of CIGS solar cells is by combining them with perovskite solar cells in tandem devices. However, so far, such tandem devices had limited efficiency due to challenges in developing NIR-transparent perovskite top cells, which allow photons with energy below the perovskite band gap to be transmitted to the bottom cell. Here, a process for the fabrication of NIR-transparent perovskite solar cells is presented, which enables power conversion efficiencies up to 12.1% combined with an average sub-band gap transmission of 71% for photons with wavelength between 800 and 1000 nm. The combination of a NIR-transparent perovskite top cell with a CIGS bottom cell enabled a tandem device with 19.5% efficiency, which is the highest reported efficiency for a polycrystalline thin film tandem solar cell. Future developments of perovskite/CIGS tandem devices are discussed and prospects for devices with efficiency toward and above 27% are given.

Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.

PubMed

Vera, Manuel; Bello, Xabier; Álvarez-Dios, Jose-Antonio; Pardo, Belen G; Sánchez, Laura; Carlsson, Jens; Carlsson, Jeanette E L; Bartolomé, Carolina; Maside, Xulio; Martinez, Paulino

2015-12-01

The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds. Copyright © 2015 Elsevier B.V. All rights reserved.

DXYS156: a multi-purpose short tandem repeat locus for determination of sex, paternal and maternal geographic origins and DNA fingerprinting.

PubMed

Calì, Francesco; Forster, P; Kersting, Christian; Mirisola, Mario G; D'Anna, Rosalba; De Leo, Giacomo; Romano, Valentino

2002-06-01

In forensic science and in legal medicine Y chromosomal typing is indispensable for sex determination, for paternity testing in the absence of the father and for distinguishing males in multiple rape cases. Another potential application is the estimation of paternal geographic origin or family name from a crime stain to narrow down the range of suspects and thus reduce costs of mass screenings. However, Y typing alone cannot provide a sufficiently resolved DNA fingerprint as required for court convictions. Thus, there is a dilemma whether or not to sacrifice valuable material for the sake of extensive Y chromosomal investigations when stain DNA is limited (typically allowing only few PCR amplifications). We here describe a Y-chromosome-specific nucleotide insertion in the duplicate short tandem repeat (STR) locus DXYS156 which allows us to distinguish males from females as does the commonly used amelogenin system, but with the advantage that this locus is multi-allelic, thus substantially contributing towards DNA fingerprinting of a sample and furthermore enabling the detection of sample contamination. Yet another bonus is that both the X and the Y copies of DXYS156 have alleles specific to different parts of the world, offering separate estimates of maternal and paternal descent of that sample. We therefore recommend the inclusion of DXYS156 in standard multiplexing kits for forensic, archaeological and genealogical applications.

Improve definition of titanium tandems in MR-guided high dose rate brachytherapy for cervical cancer using proton density weighted MRI

PubMed Central

2013-01-01

Background For cervical cancer patients treated with MR-guided high dose rate brachytherapy, the accuracy of radiation delivery depends on accurate localization of both tumors and the applicator, e.g. tandem and ovoid. Standard T2-weighted (T2W) MRI has good tumor-tissue contrast. However, it suffers from poor uterus-tandem contrast, which makes the tandem delineation very challenging. In this study, we evaluated the possibility of using proton density weighted (PDW) MRI to improve the definition of titanium tandems. Methods Both T2W and PDW MRI images were obtained from each cervical cancer patient. Imaging parameters were kept the same between the T2W and PDW sequences for each patient except the echo time (90 ms for T2W and 5.5 ms for PDW) and the slice thickness (0.5 cm for T2W and 0.25 cm for PDW). Uterus-tandem contrast was calculated by the equation C = (Su-St)/Su, where Su and St represented the average signal in the uterus and the tandem, respectively. The diameter of the tandem was measured 1.5 cm away from the tip of the tandem. The tandem was segmented by the histogram thresholding technique. Results PDW MRI could significantly improve the uterus-tandem contrast compared to T2W MRI (0.42±0.24 for T2W MRI, 0.77±0.14 for PDW MRI, p=0.0002). The average difference between the measured and physical diameters of the tandem was reduced from 0.20±0.15 cm by using T2W MRI to 0.10±0.11 cm by using PDW MRI (p=0.0003). The tandem segmented from the PDW image looked more uniform and complete compared to that from the T2W image. Conclusions Compared to the standard T2W MRI, PDW MRI has better uterus-tandem contrast. The information provided by PDW MRI is complementary to those provided by T2W MRI. Therefore, we recommend adding PDW MRI to the simulation protocol to assist tandem delineation process for cervical cancer patients. PMID:23327682

Genetic polymorphism of the 26 short tandem repeat loci in the Chinese Hebei Han population using two commercial forensic kits.

PubMed

Lei, Liang; Xu, Jie; Du, Qingqing; Fu, Lihong; Zhang, Xiaojing; Yu, Feng; Ma, Chunling; Cong, Bin; Li, Shujin

2015-01-01

We determined the allele frequencies and forensic parameters for the 26 short tandem repeat (STR) autosomal markers in two commercial kits (the Investigator HDplex and AmpFLSTR(®) Identifiler(®) systems) for 183 unrelated individuals from the Han population of the Hebei Province of China. The 26 STRs were all in Hardy-Weinberg equilibrium. No linkage disequilibrium was detected between any pair of loci. The combined power of discrimination and the combined power of exclusion for the 26 STR loci were 1-7.74E-31 and 1-1.21E-11, respectively. Six rare alleles of D10S2325 were identified and named 20, 21, 22, 23, 24, and 31. All the length of the six rare alleles were out of the range of allelic ladder. We calculated the population pairwise genetic distance based on the allele frequencies, using published population data including German, central Polish, south Dutch, northeastern Polish, south Brazilian, Korean, Sichuan Han of China, and Shanghai Han of China. Also we examined the population pairwise genetic distance of loci included in Identifiler system between Hebei Han and other ethnic population of China. These 26 autosomal STR loci could provide highly informative polymorphic data for paternity testing and forensic identification in the Hebei Han population in China. Because they are all in linkage equilibrium, they could be used together to solve deficient kinship cases or cases with mutations.

Infrared fluorescent automated detection of thirteen short tandem repeat polymorphisms and one gender-determining system of the CODIS core system.

PubMed

Ricci, U; Sani, I; Guarducci, S; Biondi, C; Pelagatti, S; Lazzerini, V; Brusaferri, A; Lapini, M; Andreucci, E; Giunti, L; Giovannucci Uzielli, M L

2000-11-01

We used an infrared (IR) automated fluorescence monolaser sequencer for the analysis of 13 autosomal short tandem repeat (STR) systems (TPOX, D3S1358, FGA, CSF1PO, D5S818, D7S820, D8S1179, TH01, vWA, D13S317, D16S359, D18S51, D21S11) and the X-Y homologous gene amelogenin system. These two systems represent the core of the combined DNA index systems (CODIS). Four independent multiplex reactions, based on the polymerase chain reaction (PCR) technique and on the direct labeling of the forward primer of every primer pair, with a new molecule (IRDye800), were set up, permitting the exact characterization of the alleles by comparison with ladders of specific sequenced alleles. This is the first report of the whole analysis of the STRs of the CODIS core using an IR automated DNA sequencer. The protocol was used to solve paternity/maternity tests and for population studies. The electrophoretic system also proved useful for the correct typing of those loci differing in size by only 2 bp. A sensibility study demonstrated that the test can detect an average of 10 pg of undegraded human DNA. We also performed a preliminary study analyzing some forensic samples and mixed stains, which suggested the usefulness of using this analytical system for human identification as well as for forensic purposes.

Flavonoid-rich cocoa consumption affects multiple cardiovascular risk factors in a meta-analysis of short-term studies.

PubMed

Shrime, Mark G; Bauer, Scott R; McDonald, Anna C; Chowdhury, Nubaha H; Coltart, Cordelia E M; Ding, Eric L

2011-11-01

A growing body of evidence suggests that the consumption of foods rich in polyphenolic compounds, particularly cocoa, may have cardioprotective effects. No review, however, has yet examined the effect of flavonoid-rich cocoa (FRC) on all major cardiovascular risk factors or has examined potential dose-response relationships for these effects. A systematic review and meta-analysis of randomized, controlled trials was performed to evaluate the effect of FRC on cardiovascular risk factors and to assess a dose-response relationship. Inclusion and exclusion criteria as well as dependent and independent variables were determined a priori. Data were collected for: blood pressure, pulse, total cholesterol, HDL cholesterol, LDL cholesterol, TG, BMI, C-reactive protein, flow-mediated vascular dilation (FMD), fasting glucose, fasting insulin, serum isoprostane, and insulin sensitivity/resistance indices. Twenty-four papers, with 1106 participants, met the criteria for final analysis. In response to FRC consumption, systolic blood pressure decreased by 1.63 mm Hg (P = 0.033), LDL cholesterol decreased by 0.077 mmol/L (P = 0.038), and HDL cholesterol increased by 0.046 mmol/L (P = 0.037), whereas total cholesterol, TG, and C-reactive protein remained the same. Moreover, insulin resistance decreased (HOMA-IR: -0.94 points; P < 0.001), whereas FMD increased (1.53%; P < 0.001). A nonlinear dose-response relationship was found between FRC and FMD (P = 0.004), with maximum effect observed at a flavonoid dose of 500 mg/d; a similar relationship may exist with HDL cholesterol levels (P = 0.06). FRC consumption significantly improves blood pressure, insulin resistance, lipid profiles, and FMD. These short-term benefits warrant larger long-term investigations into the cardioprotective role of FRC.

Tolerability and short-term effectiveness of hylan G-F 20 in 4253 patients with osteoarthritis of the knee in clinical practice.

PubMed

Kemper, Ferry; Gebhardt, Ullricht; Meng, Thomas; Murray, Christopher

2005-08-01

To determine the tolerability and short-term effectiveness of hylan G-F 20 (Synvisc) in patients with symptomatic osteoarthritis (OA) of the knee in standard clinical practice. Over 800 orthopedic surgeons in Germany recorded adverse events (AEs) for approximately five consecutive patients each following 3 weekly intra-articular hylan G-F 20 injections. Patients assessed their pain on a 4-point scale before and 3 weeks after the first injection. Potential risk factors for local AEs and possible predictors of short-term effectiveness of hylan G-F 20 were explored with logistic regression. 4253 patients were treated with 12699 injections by 840 physicians at 720 sites. Local, treatment related AEs (n = 302) were reported in 180 patients (4.2% of patients; 2.4% of injections). The most frequently reported AEs were joint effusion (2.4% of patients), joint swelling (1.3%), arthralgia (1.2%), joint warmth (0.6%), and injection site erythema (0.3%). Most AEs were mild (21.4%) to moderate (40.3%) in nature. One patient experienced a serious AE of severe swelling and synovial fluid accumulation judged as possibly treatment related. Patients < 70 years old, patients with a longer time since diagnosis, and those previously treated with visco-supplementation were more likely to experience a local AE. Pain significantly (p < 0.0001) decreased 3 weeks after the first injection compared with before treatment. Potential predictors of hylan G-F 20 short-term effectiveness were being underweight, male gender, shorter time since diagnosis, and severe baseline pain. In this population of 4253 patients treated with hylan G-F 20 for OA knee pain, the overall incidence of local, treatment-related AEs was low and consistent with those reported in the current US product labeling and previously published studies. Additionally, short-term effectiveness was confirmed.

Form-Focused Interaction in Online Tandem Learning

ERIC Educational Resources Information Center

O'Rourke, Breffni

2005-01-01

Tandem language learning--a configuration involving pairs of learners with complementary target/native languages--is an underexploited but potentially very powerful use of computer-mediated communication (CMC) in second-language pedagogy. Tandem offers the benefits of authentic, culturally grounded interaction, while also promoting a pedagogical…

Production of neutron-rich nuclei approaching r-process by gamma-induced fission of 238U at ELI-NP

NASA Astrophysics Data System (ADS)

Mei, Bo; Balabanski, Dimiter; Constantin, Paul; Anh Le, Tuan; Viet Cuong, Phan

2018-05-01

The investigation of neutron-rich exotic nuclei is crucial not only for nuclear physics but also for nuclear astrophysics. Experimentally, only few neutron-rich nuclei near the stability have been studied, however, most neutron-rich nuclei have not been measured due to their small production cross sections as well as short half-lives. At ELI-NP, gamma beams with high intensities will open new opportunities to investigate very neutron-rich fragments produced by photofission of 238U targets in a gas cell. Based on some simulations, a novel gas cell has been designed to produce, stop and extract 238U photofission fragments. The extraction time and efficiency of photofission fragments have been optimized by using SIMION simulations. According to these simulations, a high extraction efficiency and a short extraction time can be achieved for 238U photofission fragments in the gas cell, which will allow one to measure very neutron-rich fragments with short half-lives by using the IGISOL facility proposed at ELI-NP.

Electronic Tandem Language Learning (eTandem): A Third Approach to Second Language Learning for the 21st Century

ERIC Educational Resources Information Center

Cziko, Gary A.

2004-01-01

Tandem language learning occurs when two learners of different native languages work together to help each other learn the other language. First used in face-to-face contexts, Tandem is now increasingly being used by language-learning partners located in different countries who are linked via various forms of electronic communication, a context…

High efficiency thin-film crystalline Si/Ge tandem solar cell.

PubMed

Sun, G; Chang, F; Soref, R A

2010-02-15

We propose and simulate a photovoltaic solar cell comprised of Si and Ge pn junctions in tandem. With an anti-reflection film at the front surface, we have shown that optimal solar cells favor a thin Si layer and a thick Ge layer with a thin tunnel hetero-diode placed in between. We predict efficiency ranging from 19% to 28% for AM1.5G solar irradiance concentrated from 1 approximately 1000 Suns for a cell with a total thickness approximately 100 microm.

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., geographically averaged on a study-area-wide basis, that the incumbent local exchange carrier experiences based... exchange carrier experiences based on the prior year's annual use. Tandem-switched transport transmission..., geographically averaged on a study-area-wide basis, that the incumbent local exchange carrier experiences based...

Time Perspective and Identity Formation: Short-Term Longitudinal Dynamics in College Students

ERIC Educational Resources Information Center

Luyckx, Koen; Lens, Willy; Smits, Ilse; Goossens, Luc

2010-01-01

Planning for the future and developing a personalized identity are conceived of as important developmental tasks that adolescents and emerging adults are confronted with on the pathway to adulthood. The present study set out to examine whether both tasks develop in tandem by using a short-term longitudinal dataset consisting of 371 college…

Tandem catalysis: a new approach to polymers.

PubMed

Robert, Carine; Thomas, Christophe M

2013-12-21

The creation of polymers by tandem catalysis represents an exciting frontier in materials science. Tandem catalysis is one of the strategies used by Nature for building macromolecules. Living organisms generally synthesize macromolecules by in vivo enzyme-catalyzed chain growth polymerization reactions using activated monomers that have been formed within cells during complex metabolic processes. However, these biological processes rely on highly complex biocatalysts, thus limiting their industrial applications. In order to obtain polymers by tandem catalysis, homogeneous and enzyme catalysts have played a leading role in the last two decades. In the following feature article, we will describe selected published efforts to achieve these research goals.

High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation.

PubMed

Kerkour, Abdelaziz; Marquevielle, Julien; Ivashchenko, Stefaniia; Yatsunyk, Liliya A; Mergny, Jean-Louis; Salgado, Gilmar F

2017-05-12

Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element located upstream of the major transcription start site. The KRAS nuclease-hypersensitive element (NHE) region contains a G-rich element (22RT; 5'-AGGGCGGTGTGGGAATAGGGAA-3') and encompasses a Myc-associated zinc finger-binding site that regulates KRAS transcription. The NEH region therefore has been proposed as a target for new drugs that control KRAS transcription, which requires detailed knowledge of the NHE structure. In this study, we report a high-resolution NMR structure of the G-rich element within the KRAS NHE. We found that the G-rich element forms a parallel structure with three G-quartets connected by a four-nucleotide loop and two short one-nucleotide double-chain reversal loops. In addition, a thymine bulge is found between G8 and G9. The loops of different lengths and the presence of a bulge between the G-quartets are structural elements that potentially can be targeted by small chemical ligands that would further stabilize the structure and interfere or block transcriptional regulators such as Myc-associated zinc finger from accessing their binding sites on the KRAS promoter. In conclusion, our work suggests a possible new route for the development of anticancer agents that could suppress KRAS expression. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Peptide Analysis Using Tandem Mass Spectrometry

DTIC Science & Technology

1989-06-01

to give pyroglutamic acid during storage, eliminating ammonia. It is almost absent in the spectrum of a freshly-prepared sample and is not seen in...USING TANDEM MASS SPECTROMETRY INTRODUCTION S The objective of the project was to determine the complete amino acid sequence of the large polypeptide...Ubiquitin by use of fast atom bombardment (FAB) ionization and tandem mass spectrometry. The peptide containing 76 amino acid residues was available

Forensic and population genetic analysis of Xinjiang Uyghur population on 21 short tandem repeat loci of 6-dye GlobalFiler™ PCR Amplification kit.

PubMed

Zhang, Honghua; Xia, Mingying; Qi, Lijie; Dong, Lei; Song, Shuang; Ma, Teng; Yang, Shuping; Jin, Li; Li, Liming; Li, Shilin

2016-05-01

Estimating the allele frequencies and forensic statistical parameters of commonly used short tandem repeat (STR) loci of the Uyghur population, which is the fifth largest group in China, provides a more precise reference database for forensic investigation. The 6-dye GlobalFiler™ Express PCR Amplification kit incorporates 21 autosomal STRs, which have been proven that could provide reliable DNA typing results and enhance the power of discrimination. Here we analyzed the GlobalFiler STR loci on 1962 unrelated individuals from Chinese Uyghur population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were detected within and between the GlobalFiler STR loci. SE33 showed the greatest power of discrimination in Uyghur population, whereas TPOX showed the lowest. The combined power of discrimination was 99.999999999999999999999998746%. No significant difference was observed between Uyghur and the other two Uyghur populations at all tested STRs, as well as Dai and Mongolian. Significant differences were only observed between Uyghur and other Chinese populations at TH01, as well as Central-South Asian at D13S317, East Asian at TH01 and VWA. The phylogenetic analysis showed that Uyghur is genetically close to Chinese populations, as well as East Asian and Central-South Asian. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation

PubMed Central

Ichikawa, Osamu; Fujimoto, Kazushi; Yamada, Atsushi; Okazaki, Susumu; Yamazaki, Kazuto

2016-01-01

The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand—receptor interactions is complicated. Here, we identified the G-protein/β-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the β2-adrenergic receptor (β2AR) with a diverse collection of ligands and correlation analysis of their G protein/β-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the β-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/β-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs. PMID:27187591

Environmental analysis of alcohol ethoxylates and nonylphenol ethoxylate metabolites by ultra-performance liquid chromatography-tandem mass spectrometry.

PubMed

Lara-Martín, Pablo A; González-Mazo, Eduardo; Brownawell, Bruce J

2012-03-01

Surfactants and their metabolites can be found in aquatic environments at relatively high concentrations compared with other micropollutants due in part to the exceptionally large volumes produced every year. We have focused our attention here on the most widely used nonionic surfactants, alcohol ethoxylates (AEOs), and on nonylphenol ethoxylate (NPEO) degradation products (short-chain nonylphenol ethoxylates, NP1-3EO, nonylphenol, NP, and nonylphenol ethoxycarboxylates, NP1-2EC), which are endocrine-disrupting compounds. Our main objective in this work was to develop a methodology aimed at the extraction, isolation, and improved analysis of these analytes in environmental samples at trace levels. Extraction recoveries of target compounds were determined for sediment samples after ultrasonic extraction and purification using HLB or C18 solid-phase extraction minicolumns. Recovery percentages were usually between 61 and 102% but were lower for longer AEO ethoxymers. Identification and quantification of target compounds was carried out using a novel ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS-MS) approach, a combination that provides higher sensitivity and faster analysis than prior methods using conventional high-performance liquid chromatography-mass spectrometry. Limits of detection were usually below 0.5 ng/g, being higher for monoethoxylate species (>5 ng/g) because of poor ionization. The method was used for analyzing surface sediment samples collected at Jamaica Bay (NY) in 2008. The highest values (28,500 ng/g for NP, 4,200 ng/g for NP1-3EO, 22,400 ng/g for NP1-2EC, and 1,500 ng/g for AEOs) were found in a sampling station from a restricted water circulation area that is heavily impacted by wastewater discharges.

External Exposure to Short- and Medium-Chain Chlorinated Paraffins for the General Population in Beijing, China.

PubMed

Gao, Wei; Cao, Dandan; Wang, Yingjun; Wu, Jing; Wang, Ying; Wang, Yawei; Jiang, Guibin

2018-01-02

Chlorinated paraffins (CPs) are a class of compounds that are currently produced and used in large amounts in commercial products worldwide. In this study, food, indoor air, indoor dust, and drinking water samples were collected to evaluate the external exposure levels of CPs and possible pathway for the general population in Beijing, China. Short chain CPs (SCCPs) and medium chain CPs (MCCPs) in 199 samples were analyzed using a gas chromatography tandem time-of-flight high-resolution mass spectrometry (GC-TOF-HR-MS) method. High levels of CPs were observed in the indoor environment from residential houses, offices, and student dormitories. The geometric mean concentrations (GM) of ∑SCCPs and ∑MCCPs in indoor dust were 92 μg g -1 and 82 μg g -1 , respectively, while in indoor air, the concentrations were 80 ng m -3 and 3.4 ng m -3 , respectively. The GM of ∑SCCPs and ∑MCCPs in the diet were 83 ng g -1 dry weight (dw) and 56 ng g -1 dw, respectively. The most important external exposure routes to CPs to the general populations in Beijing were food intake and indoor dust ingestion. Indoor dust and indoor air posed higher risks for toddlers and infants than for adults.

Progress towards a 30% efficient GaInP/Si tandem solar cells

DOE PAGES

Essig, Stephanie; Ward, Scott; Steiner, Myles A.; ...

2015-08-28

The performance of dual-junction solar cells with a Si bottom cell has been investigated both theoretically and experimentally. Simulations show that adding a top junction with an energy bandgap of 1.6 -1.9 eV to a standard silicon solar cell enables efficiencies over 38%. Currently, top junctions of GaInP (1.8 eV) are the most promising as they can achieve 1-sun efficiencies of 20.8% [1]. We fabricated mechanically stacked, four terminal GaInP/Si tandem solar cells using a transparent adhesive between the subcells. These tandem devices achieved an efficiency of 27% under AM1.5 g spectral conditions. Furthermore, higher efficiencies can be achieved bymore » using an improved Si-bottom cell and by optimizing the dual-junction device for long-wavelength light and luminescent coupling between the two junctions.« less

Characterization of toxin-producing cyanobacteria by using an oligonucleotide probe containing a tandemly repeated heptamer.

PubMed Central

Rouhiainen, L; Sivonen, K; Buikema, W J; Haselkorn, R

1995-01-01

Cyanobacteria produce toxins that kill animals. The two main classes of cyanobacterial toxins are cyclic peptides that cause liver damage and alkaloids that block nerve transmission. Many toxin-producing strains from Finnish lakes were brought into axenic culture, and their toxins were characterized. Restriction fragment length polymorphism analysis, probing with a short tandemly repeated DNA sequence found at many locations in the chromosome of Anabaena sp. strain PCC 7120, distinguishes hepatotoxic Anabaena isolates from neurotoxin-producing strains and from Nostoc spp. PMID:7592362

Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

PubMed Central

2015-01-01

Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

TRedD—A database for tandem repeats over the edit distance

PubMed Central

Sokol, Dina; Atagun, Firat

2010-01-01

A ‘tandem repeat’ in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon the concept of ‘evolutive tandem repeats’. In addition, we have developed a tool, called TandemGraph, to graphically depict the repeats occurring in a sequence. This tool can be coupled with any repeat finding software, and it should greatly facilitate analysis of results. Database URL: http://tandem.sci.brooklyn.cuny.edu/ PMID:20624712

PTGBase: an integrated database to study tandem duplicated genes in plants.

PubMed

Yu, Jingyin; Ke, Tao; Tehrim, Sadia; Sun, Fengming; Liao, Boshou; Hua, Wei

2015-01-01

Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available. © The Author(s) 2015. Published by Oxford University Press.

Hybrid Tandem Solar Cells | Photovoltaic Research | NREL

Science.gov Websites

Hybrid Tandem Solar Cells Hybrid Tandem Solar Cells To achieve aggressive cost reductions in photovoltaics (PV) beyond the 6¢/kWh SunShot Initiative 2020 goal, module efficiency must be increased beyond on a silicon platform and that aim to provide viable prototypes for commercialization. PV Research

Inverted Three-Junction Tandem Thermophotovoltaic Modules

NASA Technical Reports Server (NTRS)

Wojtczuk, Steven

2012-01-01

An InGaAs-based three-junction (3J) tandem thermophotovoltaic (TPV) cell has been investigated to utilize more of the blackbody spectrum (from a 1,100 C general purpose heat source GPHS) efficiently. The tandem consists of three vertically stacked subcells, a 0.74-eV InGaAs cell, a 0.6- eV InGaAs cell, and a 0.55-eV InGaAs cell, as well as two interconnecting tunnel junctions. A greater than 20% TPV system efficiency was achieved by another group with a 1,040 C blackbody using a single-bandgap 0.6- eV InGaAs cell MIM (monolithic interconnected module) (30 lateral junctions) that delivered about 12 V/30 or 0.4 V/junction. It is expected that a three-bandgap tandem MIM will eventually have about 3 this voltage (1.15 V) and about half the current. A 4 A/cm2 would be generated by a single-bandgap 0.6-V InGaAs MIM, as opposed to the 2 A/cm2 available from the same spectrum when split among the three series-connected junctions in the tandem stack. This would then be about a 50% increase (3xVoc, 0.5xIsc) in output power if the proposed tandem replaced the single- bandgap MIM. The advantage of the innovation, if successful, would be a 50% increase in power conversion efficiency from radioisotope heat sources using existing thermophotovoltaics. Up to 50% more power would be generated for radioisotope GPHS deep space missions. This type of InGaAs multijunction stack could be used with terrestrial concentrator solar cells to increase efficiency from 41 to 45% or more.

Rotary-wing aircraft systems for the short-haul market

NASA Technical Reports Server (NTRS)

Magee, J. P.; Clark, R. D.; Giulianetti, D.

1975-01-01

This paper describes preliminary designs of tilt-rotor and tandem-rotor helicopter V/STOL aircraft for the 1958 short-haul market. These designs include a tilt-rotor aircraft designed for STOL-only operation. The baseline designs are presented with technological and cost data. The impact of noise and ride qualities on aircraft size and cost, and on passenger acceptance are discussed. The results of the study are compared against competitive alternatives in air transportation.

Improved purification of immunoglobulin G from plasma by mixed-mode chromatography.

PubMed

Chai, Dong-Sheng; Sun, Yan; Wang, Xiao-Ning; Shi, Qing-Hong

2014-12-01

Efficient loading of immunoglobulin G in mixed-mode chromatography is often a serious bottleneck in the chromatographic purification of immunoglobulin G. In this work, a mixed-mode ligand, 4-(1H-imidazol-1-yl) aniline, was coupled to Sepharose Fast Flow to fabricate AN SepFF adsorbents with ligand densities of 15-64 mmol/L, and the chromatographic performances of these adsorbents were thoroughly investigated to identify a feasible approach to improve immunoglobulin G purification. The results indicate that a critical ligand density exists for immunoglobulin G on the AN SepFF adsorbents. Above the critical ligand density, the adsorbents showed superior selectivity to immunoglobulin G at high salt concentrations, and also exhibited much higher dynamic binding capacities. For immunoglobulin G purification, both the yield and binding capacity increased with adsorbent ligand density along with a decrease in purity. It is difficult to improve the binding capacity, purity, and yield of immunoglobulin G simultaneously in AN SepFF chromatography. By using tandem AN SepFF chromatography, a threefold increase in binding capacity as well as high purity and yield of immunoglobulin G were achieved. Therefore, the tandem chromatography demonstrates that AN SepFF adsorbent is a practical and feasible alternative to MEP HyperCel adsorbents for immunoglobulin G purification. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Performance of a tandem-rotor/tandem-stator conical-flow compressor designed for a pressure ratio of 3

NASA Technical Reports Server (NTRS)

Wood, J. R.; Owen, A. K.; Schumann, L. F.

1982-01-01

A conical-flow compressor stage with a large radius change through the rotor was tested at three values of rotor tip clearance. The stage had a tandem rotor and a tandem stator. Peak efficiency at design speed was 0.774 at a pressure ratio of 2.613. The rotor was tested without the stator, and detailed survey data were obtained for each rotor blade row. Overall peak rotor efficiency was 0.871 at a pressure ratio of 2.952.

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed Central

Jezkova, Tereza; Wiens, John J.

2016-01-01

Animal phyla vary dramatically in species richness (from 1 species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g. sponges), parasitic worms (e.g. nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ~74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, non-marine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (~67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g. head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species. PMID:28221832

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed

Jezkova, Tereza; Wiens, John J

2017-03-01

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

Ultrafast STR Separations on Short-Channel Microfluidic Systems for Forensic Screening and Genotyping.

PubMed

Aboud, Maurice J; Gassmann, Marcus; McCord, Bruce

2015-09-01

There are situations in which it is important to quickly and positively identify an individual. Examples include suspects detained in the neighborhood of a bombing or terrorist incident, individuals detained attempting to enter or leave the country, and victims of mass disasters. Systems utilized for these purposes must be fast, portable, and easy to maintain. DNA typing methods provide the best biometric information yielding identity, kinship, and geographical origin, but they are not portable and rapid. This study details the development of a portable short-channel microfluidic device based on a modified Agilent 2100 bioanalyzer for applications in forensic genomics. The system utilizes a denaturing polymer matrix with dual-channel laser-induced fluorescence and is capable of producing a genotype in 80 sec. The device was tested for precision and resolution using an allelic ladder created from 6 short tandem repeat (STR) loci and a sex marker (amelogenin). The results demonstrated a precision of 0.09-0.21 bp over the entire size range and resolution values from 2.5 to 4.1 bp. Overall, the results demonstrate the chip provides a portable, rapid, and precise method for screening amplified short tandem repeats and human identification screening. © 2015 American Academy of Forensic Sciences.

A tandem-based compact dual-energy gamma generator.

PubMed

Persaud, A; Kwan, J W; Leitner, M; Leung, K-N; Ludewigt, B; Tanaka, N; Waldron, W; Wilde, S; Antolak, A J; Morse, D H; Raber, T

2010-02-01

A dual-energy tandem-type gamma generator has been developed at E. O. Lawrence Berkeley National Laboratory and Sandia National Laboratories. The tandem accelerator geometry allows higher energy nuclear reactions to be reached, thereby allowing more flexible generation of MeV-energy gammas for active interrogation applications. Both positively charged ions and atoms of hydrogen are created from negative ions via a gas stripper. In this paper, we show first results of the working tandem-based gamma generator and that a gas stripper can be utilized in a compact source design. Preliminary results of monoenergetic gamma production are shown.

Determination of amphetamine and methamphetamine in umbilical cord using liquid chromatography-tandem mass spectrometry

PubMed Central

Jones, Joseph; Rios, Rosemarie; Jones, Mary; Lewis, Douglas; Plate, Charles

2009-01-01

The use of meconium as a drug-screening matrix for newborns has been the gold standard of care for the past two decades. A recent study using matched pairs of meconium and umbilical cord demonstrated a high degree of agreement. The use of liquid chromatography-tandem mass spectrometry as a means to confirm amphetamines presumptive positive umbilical cord specimens for amphetamine and methamphetamine is described here for the first time. The limit of detection for both compounds was 0.2 ng/g. The limit of quantitation for both compounds was 0.6 ng/g. The assay was linear for both compounds up to 100 ng/g. PMID:19783234

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

PubMed

Sobreira, Tiago José P; Durham, Alan M; Gruber, Arthur

2006-02-01

TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

Liquid chromatography tandem mass spectrometry for the simultaneous determination of mequindox and its metabolites in porcine tissues.

PubMed

Zeng, Dongping; Shen, Xiangguang; He, Limin; Ding, Huanzhong; Tang, Youzhi; Sun, Yongxue; Fang, Binghu; Zeng, Zhenling

2012-06-01

A rapid liquid chromatography tandem mass spectrometric method was developed for the simultaneous determination of mequindox and its five metabolites (2-isoethanol mequindox, 2-isoethanol 1-desoxymequindox, 1-desoxymequindox, 1,4-bisdesoxymequindox, and 2-isoethanol bisdesoxymequindox) in porcine muscle, liver, and kidney, fulfilling confirmation criteria with two transitions for each compound with acceptable relative ion intensities. The method involved acid hydrolysis, purification by solid-phase extraction, and subsequent analysis with liquid chromatography tandem mass spectrometry using electrospray ionization operated in positive polarity with a total run time of 15 min. The decision limit values of five analytes in porcine tissues ranged from 0.6 to 2.9 μg/kg, and the detection capability values ranged from 1.2 to 5.7 μg/kg. The results of the inter-day study, which was performed by fortifying porcine muscle (2, 4, and 8 μg/kg), liver, and kidney (10, 20, and 40 μg/kg) samples on three separate days, showed that the accuracy of the method for the various analytes ranged between 75.3 and 107.2% with relative standard deviation less than 12% for each analyte. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel amphiphilic polymeric ionic liquid-solid phase micro-extraction membrane for the preconcentration of aniline as degradation product of azo dye Orange G under sonication by liquid chromatography-tandem mass spectrometry.

PubMed

Cai, Mei-Qiang; Wei, Xiao-Qing; Du, Chun-Hui; Ma, Xu-Ming; Jin, Mi-Cong

2014-07-04

A novel amphiphilic polymeric ionic liquid membrane containing a hydrophilic bromide anion and a hydrophobic carbonyl group was synthesized in dimethylformamide (DMF) systems using the ionic liquid 1-butyl-3-vinylimidazolium bromide (BVImBr) and the methylmethacrylate (MMA) as monomers. The prepared amphiphilic ploy-methylmethacrylate-1-butyl-3-vinylimidazolium bromide (MMA-BVImBr) was characterized by a scanning electron microscope and an infrared spectrum instrument. The results of solid-phase micro-extraction membrane (SPMM) experiments showed that the adsorption capacity of membrane was about 0.76μgμg(-1) for aniline. Based on this, a sensitive method for the determination of trace aniline, as a degradation product of azo dye Orange G under sonication, was developed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The calibration curve showed a good linearity ranging from 0.5 to 10.0μgL(-1) with a correlation coefficient value of 0.9998. The limit of quantification was 0.5μgL(-1). The recoveries ranged from 90.6% to 96.1%. The intra- and inter-day relative standard deviations were less than 8.3% and 10.9%. The developed SPMM-LC-MS/MS method was used successfully for preconcentration of trace aniline produced during the sonication of Orange G solution. Copyright © 2014 Elsevier B.V. All rights reserved.

A rapid gas chromatographic injection-port derivatization method for the tandem mass spectrometric determination of patulin and 5-hydroxymethylfurfural in fruit juices.

PubMed

Marsol-Vall, Alexis; Balcells, Mercè; Eras, Jordi; Canela-Garayoa, Ramon

2016-07-01

A novel method consisting of injection-port derivatization coupled to gas chromatography-tandem mass spectrometry is described. The method allows the rapid assessment of 5-hydroxymethylfurfural (HMF) and patulin content in apple and pear derivatives. The chromatographic separation of the compounds was achieved in a short chromatographic run (12.2min) suitable for routine controls of these compounds in the fruit juice industry. The optimal conditions for the injection-port derivatization were at 270°C, 0.5min purge-off, and a 1:2 sample:derivatization reagent ratio (v/v). These conditions represent an important saving in terms of derivatization reagent consumption and sample preparation time. Quality parameters were assessed for the target compounds, giving LOD of 0.7 and 1.6μg/kg and LOQ of 2 and 5μg/kg for patulin and HMF, respectively. These values are below the maximum patulin concentration in food products intended for infants and young children. Repeatability (%RSD n=5) was below 12% for both compounds. In addition, the method linearity ranged between 25 and 1000μg/kg and between 5 and 192μg/kg for HMF and patulin, respectively. Finally, the method was applied to study HMF and patulin content in various fruit juice samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

PubMed

Much, Melissa; Buza, Natalia; Hui, Pei

2014-03-01

Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

Regional and local species richness in an insular environment: Serpentine plants in California

USGS Publications Warehouse

Harrison, S.; Safford, H.D.; Grace, J.B.; Viers, J.H.; Davies, K.F.

2006-01-01

We asked how the richness of the specialized (endemic) flora of serpentine rock outcrops in California varies at both the regional and local scales. Our study had two goals: first, to test whether endemic richness is affected by spatial habitat structure (e.g., regional serpentine area, local serpentine outcrop area, regional and local measures of outcrop isolation), and second, to conduct this test in the context of a broader assessment of environmental influences (e.g., climate, soils, vegetation, disturbance) and historical influences (e.g., geologic age, geographic province) on local and regional species richness. We measured endemic and total richness and environmental variables in 109 serpentine sites (1000-m2 paired plots) in 78 serpentine-containing regions of the state. We used structural equation modeling (SEM) to simultaneously relate regional richness to regionalscale predictors, and local richness to both local-scale and regional-scale predictors. Our model for serpentine endemics explained 66% of the variation in local endemic richness based on local environment (vegetation, soils, rock cover) and on regional endemic richness. It explained 73% of the variation in regional endemic richness based on regional environment (climate and productivity), historical factors (geologic age and geographic province), and spatial structure (regional total area of serpentine, the only significant spatial variable in our analysis). We did not find a strong influence of spatial structure on species richness. However, we were able to distinguish local vs. regional influences on species richness to a novel extent, despite the existence of correlations between local and regional conditions. ?? 2006 by the Ecological Society of America.

Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat.

PubMed

Tek, Ahmet L; Kashihara, Kazunari; Murata, Minoru; Nagaki, Kiyotaka

2011-11-01

The centromere plays an essential role for proper chromosome segregation during cell division and usually harbors long arrays of tandem repeated satellite DNA sequences. Although this function is conserved among eukaryotes, the sequences of centromeric DNA repeats are variable. Most of our understanding of functional centromeres, which are defined by localization of a centromere-specific histone H3 (CENH3) protein, comes from model organisms. The components of the functional centromere in legumes are poorly known. The genus Astragalus is a member of the legumes and bears the largest numbers of species among angiosperms. Therefore, we studied the components of centromeres in Astragalus sinicus. We identified the CenH3 homolog of A. sinicus, AsCenH3 that is the most compact in size among higher eukaryotes. A CENH3-based assay revealed the functional centromeric DNA sequences from A. sinicus, called CentAs. The CentAs repeat is localized in A. sinicus centromeres, and comprises an AT-rich tandem repeat with a monomer size of 20 nucleotides.

High-performance heterostructured cathodes for lithium-ion batteries with a Ni-rich layered oxide core and a Li-rich layered oxide shell

DOE PAGES

Oh, Pilgun; Oh, Seung -Min; Li, Wangda; ...

2016-05-30

The Ni-rich layered oxides with a Ni content of >0.5 are drawing much attention recently to increase the energy density of lithium-ion batteries. However, the Ni-rich layered oxides suffer from aggressive reaction of the cathode surface with the organic electrolyte at the higher operating voltages, resulting in consequent impedance rise and capacity fade. To overcome this difficulty, we present here a heterostructure composed of a Ni-rich LiNi 0.7Co 0.15Mn 0.15O 2 core and a Li-rich Li 1.2-xNi 0.2Mn 0.6O 2 shell, incorporating the advantageous features of the structural stability of the core and chemical stability of the shell. With amore » unique chemical treatment for the activation of the Li 2MnO 3 phase of the shell, a high capacity is realized with the Li-rich shell material. Aberration-corrected scanning transmission electron microscopy (STEM) provides direct evidence for the formation of surface Li-rich shell layer. Finally, the heterostructure exhibits a high capacity retention of 98% and a discharge- voltage retention of 97% during 100 cycles with a discharge capacity of 190 mA h g -1 (at 2.0–4.5 V under C/3 rate, 1C = 200 mA g -1).« less

An oxygen-vacancy-rich Z-scheme g-C3N4/Pd/TiO2 heterostructure for enhanced visible light photocatalytic performance

NASA Astrophysics Data System (ADS)

Guo, Yanru; Xiao, Limin; Zhang, Min; Li, Qiuye; Yang, Jianjun

2018-05-01

An oxygen-vacancy-rich Z-scheme g-C3N4/Pd/TiO2 ternary nanocomposite was fabricated using nanotubular titanic acid as precursors via a simple photo-deposition of Pd nanoparticles and calcination process. The prepared nanocomposites were investigated by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, and UV-visible diffuse reflectance spectroscopy, respectively. For g-C3N4/TiO2 binary nanocomposites, at the optimal content of g-C3N4 (2%), the apparent photocatalytic activity of 2%g-C3N4/TiO2 was 9 times higher than that of pure TiO2 under visible-light illumination. After deposition of Pd (1 wt%) at the contact interface between g-C3N4 and TiO2, the 2%g-C3N4/Pd/TiO2 ternary nanocomposites demonstrated the highest visible-light-driven photocatalytic activity for the degradation of gaseous propylene, which was 16- and 2-fold higher activities than pure TiO2 and 2%g-C3N4/TiO2, respectively. The mechanism for the enhanced photocatalytic performance of the g-C3N4/Pd/TiO2 photo-catalyst is proposed to be based on the efficient separation of photo-generated electron-hole pairs through Z-scheme system, in which uniform dispersity of Pd nanoparticles at contact interface between g-C3N4 and TiO2 and oxygen vacancies promote charge separation.

Quantification of short chain amines in aqueous matrices using liquid chromatography electrospray ionization tandem mass spectrometry.

PubMed

Viidanoja, Jyrki

2017-01-13

A new liquid chromatography-electrospray ionization-tandem Mass Spectrometry (LC-ESI-MS/MS) method was developed for the determination of more than 20 C 1 -C 6 alkyl and alkanolamines in aqueous matrices. The method employs Hydrophilic Interaction Liquid Chromatography Multiple Reaction Monitoring (HILIC-MRM) with a ZIC-pHILIC column and four stable isotope labeled amines as internal standards for signal normalization and quantification of the amines. The method was validated using a refinery process water sample that was obtained from a cooling cycle of crude oil distillation. The averaged within run precision, between run precision and accuracy were generally within 2-10%, 1-9% and 80-120%, respectively, depending on the analyte and concentration level. Selected aqueous process samples were analyzed with the method. Copyright © 2016 Elsevier B.V. All rights reserved.

Evidence for human meiotic recombination interference obtained through construction of a short tandem repeat-polymorphism linkage map of chromosome 19

PubMed Central

Weber, James L.; Wang, Zhenyuan; Hansen, Kevin; Stephenson, Matt; Kappel, Clarisse; Salzman, Sherry; Wilkie, Patricia J.; Keats, Bronya; Dracopoli, Nicholas C.; Brandriff, Brigitte F.; Olsen, Anne S.

1993-01-01

An improved linkage map for human chromosome 19 containing 35 short tandem repeat polymorphisms (STRPs) and one VNTR (D19S20) was constructed. The map included 12 new (GATA)n tetranucleotide STRPs. Although total lengths of the male (114 cM) and female (128 cM) maps were similar, at both ends of the chromosome male recombination exceeded female recombination, while in the interior portion of the map female recombination was in excess. Cosmid clones containing the STRP sequences were identified and were positioned along the chromosome by fluorescent in situ hybridization. Four rounds of careful checking and removal of genotyping errors allowed biologically relevant conclusions to be made concerning the numbers and distributions of recombination events on chromosome 19. The average numbers of recombinations per chromosome matched closely the lengths of the genetic maps computed by using the program CRIMAP. Significant numbers of chromosomes with zero, one, two, or three recombinations were detected as products of both female and male meioses. On the basis of the total number of observed pairs of recombination events in which only a single informative marker was situated between the two recombinations, a maximal estimate for the rate of meiotic STRP “gene” conversion without recombination was calculated as 3 × 10−4/meiosis. For distances up to 30 cM between recombinations, many fewer chromosomes which had undergone exactly two recombinations were observed than were expected on the basis of the assumption of independent recombination locations. This strong new evidence for human meiotic interference will help to improve the accuracy of interpretation of clinical DNA test results involving polymorphisms flanking a genetic abnormality. PMID:8213834

COLDz: KARL G. JANSKY VERY LARGE ARRAY DISCOVERY OF A GAS-RICH GALAXY IN COSMOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lentati, L.; Wagg, J.; Carilli, C. L.

2015-02-10

The broad spectral bandwidth at millimeter and centimeter wavelengths provided by the recent upgrades to the Karl G. Jansky Very Large Array (VLA) has made it possible to conduct unbiased searches for molecular CO line emission at redshifts, z > 1.31. We present the discovery of a gas-rich, star-forming galaxy at z = 2.48 through the detection of CO J = 1-0 line emission in the COLDz survey and through a sensitive, Ka-band (31-39 GHz) VLA survey of a 6.5 arcmin{sup 2} region of the COSMOS field. We argue that the broad line (FWHM ∼ 570 ± 80 km s{supmore » –1}) is most likely to be CO J = 1-0 at z = 2.48, as the integrated emission is spatially coincident with an infrared-detected galaxy with a photometric redshift estimate of z {sub phot} = 3.2 ± 0.4. The CO J = 1-0 line luminosity is L{sub CO}{sup ′}=(2.2±0.3)×10{sup 10} K km s{sup –1} pc{sup 2}, suggesting a cold molecular gas mass of M {sub gas} ∼ (2-8) × 10{sup 10} M {sub ☉} depending on the assumed value of the molecular gas mass to CO luminosity ratio α{sub CO}. The estimated infrared luminosity from the (rest-frame) far-infrared spectral energy distribution (SED) is L {sub IR} = 2.5 × 10{sup 12} L {sub ☉} and the star formation rate is ∼250 M {sub ☉} yr{sup –1}, with the SED shape indicating substantial dust obscuration of the stellar light. The infrared to CO line luminosity ratio is ∼114 ± 19 L {sub ☉}/(K km s{sup –1} pc{sup 2}), similar to galaxies with similar SFRs selected at UV/optical to radio wavelengths. This discovery confirms the potential for molecular emission line surveys as a route to study populations of gas-rich galaxies in the future.« less

Alpha particle confinement in tandem mirrors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devoto, R.S.; Ohnishi, M.; Kerns, J.

1980-10-10

Mechanisms leading to loss of alpha particles from non-axisymmetric tandem mirrors are considered. Stochastic diffusion due to bounce-drift resonances, which can cause rapid radial losses of high-energy alpha particles, can be suppressed by imposing a 20% rise in axisymmetric fields before the quadrupole transition sections. Alpha particles should then be well-confined until thermal energies when they enter the resonant plateau require. A fast code for computation of drift behavior in reactors is described. Sample calculations are presented for resonant particles in a proposed coil set for the Tandem Mirror Next Step.

Tandem mobile robot system

DOEpatents

Buttz, James H.; Shirey, David L.; Hayward, David R.

2003-01-01

A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

Proceedings of the AMEDD Clinical Psychology Short Course (1987): Military Applications of Neuropsychology and Health Psychology Held in San Francisco, California on 9-13 March 1987. Volume 2.

DTIC Science & Technology

1987-07-01

R. L. Dc Valois. & L. G. ThorvI. Science. 1980 . 207. $8.) elongated receptive field with sidebands of opposite sign. In their original dis. €overyof...dependent on sensory input from the environment to trigger and shape their development (see, e.g., Chomsky, 1980 ; Pribram, 1971b). In short, there are...richness of data and theory on cerebral localization and distribution in 1980 . To his credit, Lashley recognized the problem and specified it in

On Infrared Excesses Associated with Li-Rich K Giants

NASA Technical Reports Server (NTRS)

Rebull, Luisa M.; Carlberg, Joleen K.; Gibbs, John C.; Deeb, J. Elin; Larsen, Estefania; Black, David V.; Altepeter, Shailyn; Bucksbee, Ethan; Cashen, Sarah; Clarke, Matthew;

Tandem internal models execute motor learning in the cerebellum.

PubMed

Honda, Takeru; Nagao, Soichi; Hashimoto, Yuji; Ishikawa, Kinya; Yokota, Takanori; Mizusawa, Hidehiro; Ito, Masao

2018-06-25

In performing skillful movement, humans use predictions from internal models formed by repetition learning. However, the computational organization of internal models in the brain remains unknown. Here, we demonstrate that a computational architecture employing a tandem configuration of forward and inverse internal models enables efficient motor learning in the cerebellum. The model predicted learning adaptations observed in hand-reaching experiments in humans wearing a prism lens and explained the kinetic components of these behavioral adaptations. The tandem system also predicted a form of subliminal motor learning that was experimentally validated after training intentional misses of hand targets. Patients with cerebellar degeneration disease showed behavioral impairments consistent with tandemly arranged internal models. These findings validate computational tandemization of internal models in motor control and its potential uses in more complex forms of learning and cognition. Copyright © 2018 the Author(s). Published by PNAS.

Quality evaluation of tandem mass spectral libraries.

PubMed

Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

2011-06-01

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

Nanocrystal assembly for tandem catalysis

DOEpatents

Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

2014-10-14

The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

The effects of DNA supercoiling on G-quadruplex formation.

PubMed

Sekibo, Doreen A T; Fox, Keith R

2017-12-01

Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson-Crick duplex. Quadruplex formation must therefore first require local dissociation (melting) of the duplex strands. Since negative supercoiling is known to facilitate the formation of alternative DNA structures, we have investigated G-quadruplex formation within negatively supercoiled DNA plasmids. Plasmids containing multiple copies of (G3T)n and (G3T4)n repeats, were probed with dimethylsulphate, potassium permanganate and S1 nuclease. While dimethylsulphate footprinting revealed some evidence for G-quadruplex formation in (G3T)n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed thymines in the loop regions. (G3T4)n sequences were not protected from DMS and showed no reaction with permanganate. Similarly, both S1 nuclease and 2D gel electrophoresis of DNA topoisomers did not detect any supercoil-dependent structural transitions. These results suggest that negative supercoiling alone is not sufficient to drive G-quadruplex formation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Single-task and dual-task tandem gait test performance after concussion.

PubMed

Howell, David R; Osternig, Louis R; Chou, Li-Shan

2017-07-01

To compare single-task and dual-task tandem gait test performance between athletes after concussion with controls on observer-timed, spatio-temporal, and center-of-mass (COM) balance control measurements. Ten participants (19.0±5.5years) were prospectively identified and completed a tandem gait test protocol within 72h of concussion and again 1 week, 2 weeks, 1 month, and 2 months post-injury. Seven uninjured controls (20.0±4.5years) completed the same protocol in similar time increments. Tandem gait test trials were performed with (dual-task) and without (single-task) concurrently performing a cognitive test as whole-body motion analysis was performed. Outcome variables included test completion time, average tandem gait velocity, cadence, and whole-body COM frontal plane displacement. Concussion participants took significantly longer to complete the dual-task tandem gait test than controls throughout the first 2 weeks post-injury (mean time=16.4 [95% CI: 13.4-19.4] vs. 10.1 [95% CI: 6.4-13.7] seconds; p=0.03). Single-task tandem gait times were significantly lower 72h post-injury (p=0.04). Dual-task cadence was significantly lower for concussion participants than controls (89.5 [95% CI: 68.6-110.4] vs. 127.0 [95% CI: 97.4-156.6] steps/minute; p=0.04). Moderately-high to high correlations between tandem gait test time and whole-body COM medial-lateral displacement were detected at each time point during dual-task gait (r s =0.70-0.93; p=0.03-0.001). Adding a cognitive task during the tandem gait test resulted in longer detectable deficits post-concussion compared to the traditional single-task tandem gait test. As a clinical tool to assess dynamic motor function, tandem gait may assist with return to sport decisions after concussion. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris

PubMed Central

Liachko, Ivan; Youngblood, Rachel A.; Tsui, Kyle; Bubb, Kerry L.; Queitsch, Christine; Raghuraman, M. K.; Nislow, Corey; Brewer, Bonita J.; Dunham, Maitreya J.

2014-01-01

The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins—a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation. PMID:24603708

GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

PubMed

Liachko, Ivan; Youngblood, Rachel A; Tsui, Kyle; Bubb, Kerry L; Queitsch, Christine; Raghuraman, M K; Nislow, Corey; Brewer, Bonita J; Dunham, Maitreya J

2014-03-01

The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

Short Term Objectives. (SCAT Project, Title VI-G).

ERIC Educational Resources Information Center

Archer, Anita

Developed by the staff of the SCAT (Support, Competency-Assistance and Training) Project, the document deals with the third step of the systematic instructional model--sequencing short term objectives for exceptional students. The manual focuses on reviewing long term goals established by the child study team, converting these goals into long term…

Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia.

PubMed

Gniadkowski, M; Hemmings-Mieszczak, M; Klahre, U; Liu, H X; Filipowicz, W

1996-02-15

Introns of nuclear pre-mRNAs in dicotyledonous plants, unlike introns in vertebrates or yeast, are distinctly rich in A+U nucleotides and this feature is essential for their processing. In order to define more precisely sequence elements important for intron recognition in plants, we investigated the effects of short insertions, either U-rich or A-rich, on splicing of synthetic introns in transfected protoplast of Nicotiana plumbaginifolia. It was found that insertions of U-rich (sequence UUUUUAU) but not A-rich (AUAAAAA) segments can activate splicing of a GC-rich synthetic infron, and that U-rich segments, or multimers thereof, can function irrespective of the site of insertion within the intron. Insertions of multiple U-rich segments, either at the same or different locations, generally had an additive, stimulatory effect on splicing. Mutational analysis showed that replacement of one or two U residues in the UUUUUAU sequence with A or C residues had only a small effect on splicing, but replacement with G residues was strongly inhibitory. Proteins that interact with fragments of natural and synthetic pre-mRNAs in vitro were identified in nuclear extracts of N.plumbaginifolia by UV cross- linking. The profile of cross-linked plant proteins was considerably less complex than that obtained with a HeLa cell nuclear extract. Two major cross-linkable plant proteins had apparent molecular mass of 50 and 54 kDa and showed affinity for oligouridilates present in synGC introns or for poly(U).

Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia.

PubMed Central

Gniadkowski, M; Hemmings-Mieszczak, M; Klahre, U; Liu, H X; Filipowicz, W

1996-01-01

Introns of nuclear pre-mRNAs in dicotyledonous plants, unlike introns in vertebrates or yeast, are distinctly rich in A+U nucleotides and this feature is essential for their processing. In order to define more precisely sequence elements important for intron recognition in plants, we investigated the effects of short insertions, either U-rich or A-rich, on splicing of synthetic introns in transfected protoplast of Nicotiana plumbaginifolia. It was found that insertions of U-rich (sequence UUUUUAU) but not A-rich (AUAAAAA) segments can activate splicing of a GC-rich synthetic infron, and that U-rich segments, or multimers thereof, can function irrespective of the site of insertion within the intron. Insertions of multiple U-rich segments, either at the same or different locations, generally had an additive, stimulatory effect on splicing. Mutational analysis showed that replacement of one or two U residues in the UUUUUAU sequence with A or C residues had only a small effect on splicing, but replacement with G residues was strongly inhibitory. Proteins that interact with fragments of natural and synthetic pre-mRNAs in vitro were identified in nuclear extracts of N.plumbaginifolia by UV cross- linking. The profile of cross-linked plant proteins was considerably less complex than that obtained with a HeLa cell nuclear extract. Two major cross-linkable plant proteins had apparent molecular mass of 50 and 54 kDa and showed affinity for oligouridilates present in synGC introns or for poly(U). PMID:8604302

Negotiating Multiple Identities through eTandem Learning Experiences

ERIC Educational Resources Information Center

Yang, Se Jeong; Yi, Youngjoo

2017-01-01

Much of eTandem research has investigated either linguistic or cross-cultural aspects of second language (L2) learning, but relatively little is known about issues of identity construction in an eTandem context. Situating the study within theories and research of language learner identity, we examined ways in which two adult L2 learners (a Korean…

Low temperature perovskite solar cells with an evaporated TiO 2 compact layer for perovskite silicon tandem solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bett, Alexander J.; Schulze, Patricia S. C.; Winkler, Kristina

Silicon-based tandem solar cells can overcome the efficiency limit of single junction silicon solar cells. Perovskite solar cells are particularly promising as a top cell in monolithic tandem devices due to their rapid development towards high efficiencies, a tunable band gap with a sharp optical absorption edge and a simple production process. In monolithic tandem devices, the perovskite solar cell is deposited directly on the silicon cell, requiring low-temperature processes (< 200 °C) to maintain functionality of under-lying layers of the silicon cell in case of highly efficient silicon hetero-junction (SHJ) bottom solar cell. In this work, we present amore » complete low-temperature process for perovskite solar cells including a mesoporous titanium oxide (TiO 2) scaffold - a structure yielding the highest efficiencies for single-junction perovskite solar cells. We show that evaporation of the compact TiO 2 hole blocking layer and ultra-violet (UV) curing for the mesoporous TiO 2 layer allows for good performance, comparable to high-temperature (> 500 °C) processes. With both manufacturing routes, we obtain short-circuit current densities (J SC) of about 20 mA/cm 2, open-circuit voltages (V OC) over 1 V, fill factors (FF) between 0.7 and 0.8 and efficiencies (n) of more than 15%. We further show that the evaporated TiO 2 layer is suitable for the application in tandem devices. The series resistance of the layer itself and the contact resistance to an indium doped tin oxide (ITO) interconnection layer between the two sub-cells are low. Additionally, the low parasitic absorption for wavelengths above the perovskite band gap allow a higher absorption in the silicon bottom solar cell, which is essential to achieve high tandem efficiencies.« less

Low temperature perovskite solar cells with an evaporated TiO 2 compact layer for perovskite silicon tandem solar cells

DOE PAGES

Bett, Alexander J.; Schulze, Patricia S. C.; Winkler, Kristina; ...

2017-09-21

Silicon-based tandem solar cells can overcome the efficiency limit of single junction silicon solar cells. Perovskite solar cells are particularly promising as a top cell in monolithic tandem devices due to their rapid development towards high efficiencies, a tunable band gap with a sharp optical absorption edge and a simple production process. In monolithic tandem devices, the perovskite solar cell is deposited directly on the silicon cell, requiring low-temperature processes (< 200 °C) to maintain functionality of under-lying layers of the silicon cell in case of highly efficient silicon hetero-junction (SHJ) bottom solar cell. In this work, we present amore » complete low-temperature process for perovskite solar cells including a mesoporous titanium oxide (TiO 2) scaffold - a structure yielding the highest efficiencies for single-junction perovskite solar cells. We show that evaporation of the compact TiO 2 hole blocking layer and ultra-violet (UV) curing for the mesoporous TiO 2 layer allows for good performance, comparable to high-temperature (> 500 °C) processes. With both manufacturing routes, we obtain short-circuit current densities (J SC) of about 20 mA/cm 2, open-circuit voltages (V OC) over 1 V, fill factors (FF) between 0.7 and 0.8 and efficiencies (n) of more than 15%. We further show that the evaporated TiO 2 layer is suitable for the application in tandem devices. The series resistance of the layer itself and the contact resistance to an indium doped tin oxide (ITO) interconnection layer between the two sub-cells are low. Additionally, the low parasitic absorption for wavelengths above the perovskite band gap allow a higher absorption in the silicon bottom solar cell, which is essential to achieve high tandem efficiencies.« less

Tandem robot control system and method for controlling mobile robots in tandem

DOEpatents

Hayward, David R.; Buttz, James H.; Shirey, David L.

2002-01-01

A control system for controlling mobile robots provides a way to control mobile robots, connected in tandem with coupling devices, to navigate across difficult terrain or in closed spaces. The mobile robots can be controlled cooperatively as a coupled system in linked mode or controlled individually as separate robots.

SYMTRAN - A Time-dependent Symmetric Tandem Mirror Transport Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hua, D; Fowler, T

2004-06-15

A time-dependent version of the steady-state radial transport model in symmetric tandem mirrors in Ref. [1] has been coded up and first tests performed. Our code, named SYMTRAN, is an adaptation of the earlier SPHERE code for spheromaks, now modified for tandem mirror physics. Motivated by Post's new concept of kinetic stabilization of symmetric mirrors, it is an extension of the earlier TAMRAC rate-equation code omitting radial transport [2], which successfully accounted for experimental results in TMX. The SYMTRAN code differs from the earlier tandem mirror radial transport code TMT in that our code is focused on axisymmetric tandem mirrorsmore » and classical diffusion, whereas TMT emphasized non-ambipolar transport in TMX and MFTF-B due to yin-yang plugs and non-symmetric transitions between the plugs and axisymmetric center cell. Both codes exhibit interesting but different non-linear behavior.« less

Overlooked Short Toxin-Like Proteins: A Shortcut to Drug Design

PubMed Central

Linial, Michal

2017-01-01

Short stable peptides have huge potential for novel therapies and biosimilars. Cysteine-rich short proteins are characterized by multiple disulfide bridges in a compact structure. Many of these metazoan proteins are processed, folded, and secreted as soluble stable folds. These properties are shared by both marine and terrestrial animal toxins. These stable short proteins are promising sources for new drug development. We developed ClanTox (classifier of animal toxins) to identify toxin-like proteins (TOLIPs) using machine learning models trained on a large-scale proteomic database. Insects proteomes provide a rich source for protein innovations. Therefore, we seek overlooked toxin-like proteins from insects (coined iTOLIPs). Out of 4180 short (<75 amino acids) secreted proteins, 379 were predicted as iTOLIPs with high confidence, with as many as 30% of the genes marked as uncharacterized. Based on bioinformatics, structure modeling, and data-mining methods, we found that the most significant group of predicted iTOLIPs carry antimicrobial activity. Among the top predicted sequences were 120 termicin genes from termites with antifungal properties. Structural variations of insect antimicrobial peptides illustrate the similarity to a short version of the defensin fold with antifungal specificity. We also identified 9 proteins that strongly resemble ion channel inhibitors from scorpion and conus toxins. Furthermore, we assigned functional fold to numerous uncharacterized iTOLIPs. We conclude that a systematic approach for finding iTOLIPs provides a rich source of peptides for drug design and innovative therapeutic discoveries. PMID:29109389

Simulation study of GaAsP/Si tandem cells including the impact of threading dislocations on the luminescent coupling between the cells

NASA Astrophysics Data System (ADS)

Onno, Arthur; Harder, Nils-Peter; Oberbeck, Lars; Liu, Huiyun

2016-03-01

A model, derived from the detailed balance model from Shockley and Queisser, has been adapted to monolithically grown GaAsP/Si tandem dual junction solar cells. In this architecture, due to the difference of lattice parameters between the silicon bottom cell - acting as the substrate - and the GaAsP top cell, threading dislocations (TDs) arise at the IIIV/ Si interface and propagate in the top cell. These TDs act as non-radiative recombination centers, degrading the performances of the tandem cell. Our model takes into account the impact of TDs by integrating the NTT model developed by Yamaguchi et. al.. Two surface geometries have been investigated: flat and ideally textured. Finally the model considers the luminescent coupling (LC) between the cells due to reemitted photons from the top cell cascading to the bottom cell. Without dislocations, LC allows a greater flexibility in the cell design by rebalancing the currents between the two cells when the top cell presents a higher short-circuit current. However we show that, as the TD density (TDD) increases, nonradiative recombinations take over radiative recombinations in the top cell and the LC is quenched. As a result, nonoptimized tandem cells with higher short-circuit current in the top cell experience a very fast degradation of efficiency for TDDs over 104cm-2. On the other hand optimized cells with matching currents only experience a small efficiency drop for TDDs up to 105cm-2. High TDD cells therefore need to be current-matched for optimal performances as the flexibility due to LC is lost.

Simultaneous determination of three pesticides and their metabolites in unprocessed foods using ultraperformance liquid chromatography-tandem mass spectrometry.

PubMed

Rong, Lili; Wu, Xiaohu; Xu, Jun; Dong, Fengshou; Liu, Xingang; Pan, Xinglu; Du, Pengqiang; Wei, Dongmei; Zheng, Yongquan

2018-02-01

We have developed a rapid, multi-compound analytical method for measuring residues of the pesticides thiamethoxam and its metabolite, clothianidin; fipronil and its three metabolites, fipronil sulfone, fipronil sulfide, and fipronil desulfinyl; and pyraclostrobin in unprocessed foods (rice, corn, cucumbers, tomatoes, apples, and bananas) by ultra-performance liquid chromatography coupled to tandem mass spectrometry. Acetonitrile was used as the extraction solvent, and an octadecylsilane-dispersive SPE was used to clean up the analytes, which were then separated through a UPLC HSS T3 column connected to a tandem mass spectrometer via an electrospray ionisation source. The linearity of this method for the target analytes was excellent (R 2  ≥0.990) in the concentration range of 5-1000 μg kg -1 . The average recoveries of the seven compounds at concentrations of 10, 100, and 1000 μg kg -1 from six spiked matrix samples ranged from 73.6 to 110.6%, all with RSD values of ≤19.7%. The limit of quantification was 10 μg kg -1 . The method validated the effectiveness of the method for routine monitoring the residue of these pesticides and their metabolites in foods.

The production and characterization of novel heavy-chain antibodies against the tandem repeat region of MUC1 mucin.

PubMed

Rahbarizadeh, Fatemeh; Rasaee, Mohammad J; Forouzandeh, Mehdi; Allameh, Abdolamir; Sarrami, Ramin; Nasiry, Habib; Sadeghizadeh, Majid

2005-01-01

Camelidae are known to produce immunoglobulins (Igs) devoid of light chains and constant heavy-chain domains (CH1). Antigen-specific fragments of these heavy-chain IgGs (VHH) are of great interest in biotechnology applications. This paper describes the first example of successfully raised heavy-chain antibodies in Camelus dromedarius (single-humped camel) and Camelus bactrianus (two-humped camel) against a MUC1 related peptide that is found to be an important epitope expressed in cancerous tissue. Camels were immunized against a synthetic peptide corresponding to the tandem repeat region of MUC1 mucin and cancerous tissue preparation obtained from patients suffering from breast carcinoma. Three IgG subclasses with different binding properties to protein A and G were purified by affinity chromatography. Both conventional and heavy-chain IgG antibodies were produced in response to MUC1-related peptide. The elicited antibodies could react specifically with the tandem repeat region of MUC1 mucin in an enzyme linked immunosorbant assay (ELISA). Anti-peptide antibodies were purified after passing antiserum over two affinity chromatography columns. Using ELISA, immunocytochemistry and Western blotting, the interaction of purified antibodies with different antigens was evaluated. The antibodies were observed to be selectively bound to antigens namely: MUC1 peptide (tandem repeat region), human milk fat globule membrane (HMFG), deglycosylated human milk fat globule membrane (D-HMFG), homogenized cancerous breast tissue and a native MUC1 purified from ascitic fluid. Ka values of specific polyclonal antipeptide antibodies were estimated in C. dromedarius and C. bactrianus, as 7 x 10(10) M(-1) and 1.4 x 10(10) M(-1) respectively.

Cooperative cell motility during tandem locomotion of amoeboid cells

PubMed Central

Bastounis, Effie; Álvarez-González, Begoña; del Álamo, Juan C.; Lasheras, Juan C.; Firtel, Richard A.

2016-01-01

Streams of migratory cells are initiated by the formation of tandem pairs of cells connected head to tail to which other cells subsequently adhere. The mechanisms regulating the transition from single to streaming cell migration remain elusive, although several molecules have been suggested to be involved. In this work, we investigate the mechanics of the locomotion of Dictyostelium tandem pairs by analyzing the spatiotemporal evolution of their traction adhesions (TAs). We find that in migrating wild-type tandem pairs, each cell exerts traction forces on stationary sites (∼80% of the time), and the trailing cell reuses the location of the TAs of the leading cell. Both leading and trailing cells form contractile dipoles and synchronize the formation of new frontal TAs with ∼54-s time delay. Cells not expressing the lectin discoidin I or moving on discoidin I–coated substrata form fewer tandems, but the trailing cell still reuses the locations of the TAs of the leading cell, suggesting that discoidin I is not responsible for a possible chemically driven synchronization process. The migration dynamics of the tandems indicate that their TAs’ reuse results from the mechanical synchronization of the leading and trailing cells’ protrusions and retractions (motility cycles) aided by the cell–cell adhesions. PMID:26912787

DNA Damage by Ionizing Radiation: Tandem Double Lesions by Charged Particles

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Chaban, Galina M.; Wang, Dunyou; Dateo, Christopher E.

2005-01-01

Oxidative damages by ionizing radiation are the source of radiation-induced carcinogenesis, damage to the central nervous system, lowering of the immune response, as well as other radiation-induced damages to human health. Monte Carlo track simulations and kinetic modeling of radiation damages to the DNA employ available molecular and cellular data to simulate the biological effect of high and low LET radiation io the DNA. While the simulations predict single and double strand breaks and base damages, so far all complex lesions are the result of stochastic coincidence from independent processes. Tandem double lesions have not yet been taken into account. Unlike the standard double lesions that are produced by two separate attacks by charged particles or radicals, tandem double lesions are produced by one single attack. The standard double lesions dominate at the high dosage regime. On the other hand, tandem double lesions do not depend on stochastic coincidences and become important at the low dosage regime of particular interest to NASA. Tandem double lesions by hydroxyl radical attack of guanine in isolated DNA have been reported at a dosage of radiation as low as 10 Gy. The formation of two tandem base lesions was found to be linear with the applied doses, a characteristic of tandem lesions. However, tandem double lesions from attack by a charged particle have not been reported.

Tetramer-organizing polyproline-rich peptides differ in CHO cell-expressed and plasma-derived human butyrylcholinesterase tetramers.

PubMed

Schopfer, Lawrence M; Lockridge, Oksana

2016-06-01

Tetrameric butyrylcholinesterase (BChE) in human plasma is the product of multiple genes, namely one BCHE gene on chromosome 3q26.1 and multiple genes that encode polyproline-rich peptides. The function of the polyproline-rich peptides is to assemble BChE into tetramers. CHO cells transfected with human BChE cDNA express BChE monomers and dimers, but only low quantities of tetramers. Our goal was to identify the polyproline-rich peptides in CHO-cell derived human BChE tetramers. CHO cell-produced human BChE tetramers were purified from serum-free culture medium. Peptides embedded in the tetramerization domain were released from BChE tetramers by boiling and identified by liquid chromatography-tandem mass spectrometry. A total of 270 proline-rich peptides were sequenced, ranging in size from 6-41 residues. The peptides originated from 60 different proteins that reside in multiple cell compartments including the nucleus, cytoplasm, and endoplasmic reticulum. No single protein was the source of the polyproline-rich peptides in CHO cell-expressed human BChE tetramers. In contrast, 70% of the tetramer-organizing peptides in plasma-derived BChE tetramers originate from lamellipodin. No protein source was identified for polyproline peptides containing up to 41 consecutive proline residues. In conclusion, the use of polyproline-rich peptides as a tetramerization motif is documented only for the cholinesterases, but is expected to serve other tetrameric proteins as well. The CHO cell data suggest that the BChE tetramer-organizing peptide can arise from a variety of proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

KinG Is a Plant-Specific Kinesin That Regulates Both Intra- and Intercellular Movement of SHORT-ROOT.

PubMed

Spiegelman, Ziv; Lee, Chin-Mei; Gallagher, Kimberly L

2018-01-01

Both endogenous plant proteins and viral movement proteins associate with microtubules to promote their movement through plasmodesmata. The association of viral movement proteins with microtubules facilitates the formation of virus-associated replication complexes, which are required for the amplification and subsequent spread of the virus. However, the role of microtubules in the intercellular movement of plant proteins is less clear. Here we show that the SHORT-ROOT (SHR) protein, which moves between cells in the root to regulate root radial patterning, interacts with a type-14 kinesin, KINESIN G (KinG). KinG is a calponin homology domain kinesin that directly interacts with the SHR-binding protein SIEL (SHR-INTERACING EMBRYONIC LETHAL) and localizes to both microtubules and actin. Since SIEL and SHR associate with endosomes, we suggest that KinG serves as a linker between SIEL, SHR, and the plant cytoskeleton. Loss of KinG function results in a decrease in the intercellular movement of SHR and an increase in the sensitivity of SHR movement to treatment with oryzalin. Examination of SHR and KinG localization and dynamics in live cells suggests that KinG is a nonmotile kinesin that promotes the pausing of SHR-associated endosomes. We suggest a model in which interaction of KinG with SHR allows for the formation of stable movement complexes that facilitate the cell-to-cell transport of SHR. © 2018 American Society of Plant Biologists. All Rights Reserved.

A tandem mirror hybrid plume plasma propulsion facility

NASA Technical Reports Server (NTRS)

Yang, T. F.; Krueger, W. A.; Peng, S.; Urbahn, J.; Chang-Diaz, F. R.

1988-01-01

This paper discusses a novel concept in electrodeless plasma propulsion, in which the materials problems are ameliorated by an electrodeless magnetic confinement scheme borrowed from the tandem mirror approach to controlled thermonuclear fusion. The concept also features a two-stage magnetic nozzle with an annular hypersonic coaxial gas injector near the throat. The nozzle produces hybrid plume by the coaxial injection of hypersonic neutral gas, and the gas layer thus formed protects the material walls from the hot plasma and, through increased collisions, helps detach it from the diverging magnetic field. The tandem mirror plasma propulsion facility is capable of delivering a variable I(sp). The results of numerical simulation of this concept are presented together with those from an experimental tandem-mirror plasma propulsion device.

Ultra-high-pressure liquid chromatography-tandem mass spectrometry method for the determination of alkylphenols in soil.

PubMed

Wang, Jing; Pan, Hefang; Liu, Zhengzheng; Ge, Fei

2009-03-20

A novel method has been developed for the determination of alkylphenols in soil by ultra-high-pressure liquid chromatography employing small particle sizes, combined with tandem mass spectrometry. Soil samples were extracted with pressurized liquid extraction (PLE) and then cleaned with solid-phase extraction (SPE). The extracts were separated on C18 column (1.7 microm, 50 mm x 2.1mm) with a gradient elution and a mobile phase consisting of water and acetonitrile, and then detected by an electrospray ionization tandem mass spectrometry in negative ion mode with multiple reaction monitoring (MRM). Compared with traditional liquid chromatography, it took ultra-high-pressure liquid chromatography much less time to analyze alkylphenols. Additionally, the ultra-high-pressure liquid chromatography/tandem mass spectrometry method produces satisfactory reliability, sensitivity, and accuracy. The average recoveries of the three target analytes were 74.0-103.4%, with the RSD<15%. The calibration curves for alkylphenols were linear within the range of 0.01-0.4 microg/ml, with the correlation coefficients greater than 0.99. When 10 g soil sample was used for analysis, the limits of quantification (LOQs) of the three alkylphenols were all 1.0 microg/kg.

Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China.

PubMed

Shi, Yunfang; Li, Xiaozhou; Ju, Duan; Li, Yan; Zhang, Xiuling; Zhang, Ying

2015-08-01

Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24-48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome.

Rapid residue analysis of four triazolopyrimidine herbicides in soil, water, and wheat by ultra-performance liquid chromatography coupled to tandem mass spectrometry.

PubMed

Liu, Xingang; Xu, Jun; Li, Yuanbo; Dong, Fengshou; Li, Jing; Song, Wenchen; Zheng, Yongquan

2011-03-01

A sensitive and effective method for simultaneous determination of triazolopyrimidine sulfonamide herbicide residues in soil, water, and wheat was developed using ultra-performance liquid chromatography coupled with tandem mass spectrometry. The four herbicides (pyroxsulam, flumetsulam, metosulam, and diclosulam) were cleaned up with an off-line C18 SPE cartridge and detected by tandem mass spectrometry using an electrospray ionization source in positive mode (ESI+). The determination of the target compounds was achieved in <2.0 min. The limits of detection were below 1 μg kg(-1), while the limits of quantification did not exceed 3 μg kg(-1) in different matrices. Quantitation was determined from calibration curves of standards containing 0.05-100 μg L(-1) with r(2) > 0.997. Recovery studies were conducted at three spiked levels (0.2, 1, and 5 μg kg(-1) for water; 5, 10, and 100 μg kg(-1) for soil and wheat). The overall average recoveries for this method in water, soil, wheat plants, and seeds at three levels ranged from 75.4% to 106.0%, with relative standard deviations in the range of 2.1-12.5% (n = 5) for all analytes.

May flood-poor periods be more dangerous than flood-rich periods?

NASA Astrophysics Data System (ADS)

Salinas, Jose Luis; Di Baldassarre, Giuliano; Viglione, Alberto; Kuil, Linda; Bloeschl, Guenter

2014-05-01

perception of risk and, consequently, people preparedness remains high. Conversely, long periods without floods will serve to diminish awareness, since the memory of floods tends to be short (i.e., people tend to forget quickly), finally leading communities to take too high risks. Di Baldassarre, G., A. Viglione, G. Carr, L. Kuil, J.L. Salinas and G. Blöschl (2013) Socio-hydrology: conceptualising human-flood interactions, Hydrology and Earth System Sciences, 17, 3295-3303, doi:10.5194/hess-17-3295-2013. Viglione, A., G. Di Baldassarre, L. Brandimarte, L. Kuil, G. Carr, J.L. Salinas, A. Scolobig and G. Blöschl (2013) Insights from socio-hydrology modelling on dealing with flood risk: roles of collective memory, risk-taking attitude and trust, Journal of Hydrology, accepted.

Biosignatures Preservation Potential and Habitability in Phyllosilicates vs. Iron-rich Environments

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.; McKay, C. P.; Science Team

2008-12-01

Phyllosilicates have been identified on the surface of Mars by the OMEGA-Mars/Express [e.g., 1], the Mars Reconnaissance Orbiter (MRO) instruments, i.e., HiRISE and CRISM, as well as inferred from rover observations in Gusev Crater [2]). A better understanding of the preservation potential and habitability in phyllosilicates and hematite-rich materials, achieved by studying analog sites, will therefore provide critical information in support of next decade missions landing site selection e.g., 2009 Mars Science Laboratory (MSL), the ESA Pasteur ExoMars. We present geochemical (d13C-org, d13N-tot, CN ratios) and microbiological proxies i.e., Adenosin-Triphosphate (ATP-based) and Limulus-Amebocite-Lysate (LAL-based biomass) from a suite of phyllosilicate and iron-rich environmental samples e.g., Rio Tinto (Spain), Death Valley (CA, USA), Atacama Desert (Chile), and the California coast. Phyllosilicates-rich zones (47-74wt.%) from the Rio Tinto (RT) region can preserve up to 10-time higher amount of organics (C-org = 0.23 wt.%) than the embedding hematite/goethite-rich (34-89 wt.%) rocks i.e., C-org: ~0.05 wt.% [4]. It is possible that under low pH and highly oxidizing conditions [e.g., 3] surface-derived organics are rapidly oxidized within the shallow hematite/goethite-rich materials, but preserved in phyllosilicates (smectites/illite) where conditions are more conducive [4]. ATP-based biomass was detected in some oxidized-rock samples where roots materials were present (750-1245 RLUs). Geochemical and microbiological analyses are underway to confirm the preservation/ habitability trends observed in the Rio Tinto near surface. Preliminary results suggest that oxidized, goethite-rich, sandstone (Purisima formation, CA) have higher ATP- and LAL-based (Gram negative) biomass contents i.e., 2.0 107 cell/g (35.05 EU/mL) and 3891 RLUs, than the overlying clays units i.e., 1.34 107 cell/g (22.0EU/mL) and 1143 RLUs. REFERENCES: [1] Bibring et al., 2006, Science 312

Monitoring Bilingualism: Pedagogical Implications of the Bilingual Tandem Analyser

ERIC Educational Resources Information Center

Schwienhorst, Klaus; Borgia, Alexandre

2006-01-01

Tandem learning is the collaborative learning partnership of two language learners with complementary language combinations, for example an Irish student learning German and a German student learning English. One of the major principles in tandem learning, apart from reciprocity and learner autonomy, is balanced bilingualism. While learners may…

The -675 4G/5G polymorphism at the Plasminogen Activator Inhibitor 1 (PAI-1) gene modulates plasma Plasminogen Activator Inhibitor 1 concentrations in response to dietary fat consumption.

PubMed

Pérez-Martínez, P; Adarraga-Cansino, M D; Fernández de la Puebla, R A; Blanco-Molina, A; Delgado-Lista, J; Marín, C; Ordovás, J M; López-Miranda, J; Pérez-Jiménez, F

2008-04-01

The objective of the study was to determine whether Plasminogen Activator Inhibitor Type 1 (PAI-1) -675 4G/5G polymorphism is associated with the response of functional plasma PAI-1 concentrations to changes in the amount and quality of dietary fat in healthy subjects. PAI-1 is the major inhibitor of fibrinolysis, and a lower level of fibrinolytic activity could be implicated in an increased risk of IHD. Fifty-nine healthy Spanish volunteers (ten 4G/4G homozygotes, twenty-eight heterozygotes 4G/5G and twenty-one 5G/5G homozygotes) consumed three diets for periods of 4 weeks each: a SFA-rich diet (38 % fat, 20 % SFA), followed by a carbohydrate-rich diet (30 % fat, 55 % carbohydrate) and a MUFA-rich diet (38 % fat, 22 % MUFA) according to a randomized crossover design. At the end of each dietary period plasma lipid and functional plasma PAI-1 concentrations were determined. Subjects carrying the 4G allele (4G/4G and 4G/5G) showed a significant decrease in PAI-1 concentrations after the MUFA diet, compared with the SFA-rich and carbohydrate-rich diets (genotype x diet interaction: P = 0.028). 5G/5G homozygotes had the lowest plasma PAI-1 concentrations compared with 4G/4G and 4G/5G subjects (genotype: P = 0.002), without any changes as a result of the amount and the quality of the dietary fat. In summary, no differences in plasma PAI-1 concentration response were found after changes in dietary fat intake in 5G/5G homozygotes, although these subjects displayed the lowest concentrations of PAI-1. On the other hand, carriers of the 4G allele are more likely to hyper-respond to the presence of MUFA in the diet because of a greater decrease in PAI-1 concentrations.

High Performance Tandem Perovskite/Polymer Solar Cells

NASA Astrophysics Data System (ADS)

Liu, Yao; Bag, Monojit; Page, Zachariah; Renna, Lawrence; Kim, Paul; Choi, Jaewon; Emrick, Todd; Venkataraman, D.; Russell, Thomas

Combining perovskites with other inorganic materials, such as copper indium gallium diselenide (CIGS) or silicon, is enabling significant improvement in solar cell device performance. Here, we demonstrate a highly efficient hybrid tandem solar cell fabricated through a facile solution deposition approach to give a perovskite front sub-cell and a polymer:fullerene blend back sub-cell. This methodology eliminates the adverse effects of thermal annealing during perovskite fabrication on polymer solar cells. The record tandem solar cell efficiency of 15.96% is 40% greater than the corresponding perovskite-based single junction device and 65% greater than the polymer-based single junction device, while mitigating deleterious hysteresis effects often associated with perovskite solar cells. The hybrid tandem devices demonstrate the synergistic effects arising from the combination of perovskite and polymer-based materials for solar cells. This work was supported by the Department of Energy-supported Energy Frontier Research Center at the University of Massachusetts (DE-SC0001087). The authors acknowledge the W.M. Keck Electron Microscopy.

Rapid and sensitive determination of benzo[a]pyrene in black ginseng using fluorescence detector and high performance liquid chromatography-tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Cho, Hyun-jeong; Kim, Hye-jin; Son, Byeong-cheol; Jo, Dong-keun; Cho, Byung-lim

2013-05-01

Black ginseng is produced by steaming a ginseng root followed by drying repeatedly 9 times during the process and it is changed to be black color, so it is known that a black ginseng has more contents of saponins than red ginseng. However a fake black ginseng which is produced to be black color at high temperature in a short period of time generate carcinogenic benzo[a]pyrene(BaP) through the process. In this year, maximum residue level(MRL) for BaP was established to 2 ug/kg in black ginseng and more sensitive method was developed to quantitatively analyze the BaP by high performance liquid chromatography (HPLC) coupling with florescence detector and tandem mass spectrometry (atmospheric pressure chemical ionization-MS/MS). Chromatographic separation was performed on a Supelcosil™ LC-PAH column (3 μm, 3 mm x 50 mm). Mobile phase A was water and mobile phase B was acetonitrile. BaP was exactly separated from other 15 polycyclic aromatic hydrocarbons (PAHs) which have been selected as priority pollutants by the US Environmental Protection Agency (EPA). Linearity of detection was in the range of 0.2~20 μg/kg and limit of detection (LOD) for BaP was lower than 0.1 μg/kg, limit of quantification (LOQ) was 0.2 μg/kg. The recovery of Bap was 92.54%+/-6.3% in black ginseng.

rTANDEM, an R/Bioconductor package for MS/MS protein identification.

PubMed

Fournier, Frédéric; Joly Beauparlant, Charles; Paradis, René; Droit, Arnaud

2014-08-01

rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Dispersive solid-phase extraction followed by high-performance liquid chromatography/tandem mass spectrometry for the determination of ricinine in cooking oil.

PubMed

Cai, Meiqiang; Chen, Xiaohong; Wei, Xiaoqing; Pan, Shengdong; Zhao, Yonggang; Jin, Micong

2014-09-01

A rapid and accurate method by liquid chromatography/tandem mass spectrometry (LC-MS/MS) using positive electrospray was established for the determination of ricinine in cooking oils. The homogenized samples, spiked with (13)C6-labelled ricinine as an internal standard, were extracted using ethanol/water (20:80, v/v) and purified by dispersive solid-phase extraction (dSPE) using primary-secondary amine (PSA) and C18 as adsorbents. The extract was separated in a short C18 reversed-phase column using methanol/water (25:75, v/v) as the mobile phase and detected in multiple reaction monitoring (MRM) mode with the absolute matrix effect of 93.2-102.2%. The alkali-metal adduct ions were discussed and the mass/mass fragmentation pathway was explained. Ricinine showed good linearity in the range of 0.5-50.0 μg/kg with the limit of quantitation 0.5 μg/kg. The recoveries were between 86.0% and 98.3% with the intra- and inter-day RSDs of 2.6-7.0%, 5.5-10.8%, respectively. This method could be applied to the rapid quantification of ricinine in cooking oils. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Semi-transparent perovskite solar cells for tandems with silicon and CIGS

DOE PAGES

Bailie, Colin D.; Christoforo, M. Greyson; Mailoa, Jonathan P.; ...

2014-12-23

A promising approach for upgrading the performance of an established low-bandgap solar technology without adding much cost is to deposit a high bandgap polycrystalline semiconductor on top to make a tandem solar cell. We use a transparent silver nanowire electrode on perovskite solar cells to achieve a semi-transparent device. We place the semi-transparent cell in a mechanically-stacked tandem configuration onto copper indium gallium diselenide (CIGS) and low-quality multicrystalline silicon (Si) to achieve solid-state polycrystalline tandem solar cells with a net improvement in efficiency over the bottom cell alone. Furthermore, this work paves the way for integrating perovskites into a low-costmore » and high-efficiency (>25%) tandem cell.« less

Direct determination of trace phthalate esters in alcoholic spirits by spray-inlet microwave plasma torch ionization tandem mass spectrometry.

PubMed

Miao, Meng; Zhao, Gaosheng; Xu, Li; Dong, Junguo; Cheng, Ping

2018-03-01

A direct analytical method based on spray-inlet microwave plasma torch tandem mass spectrometry was applied to simultaneously determine 4 phthalate esters (PAEs), namely, benzyl butyl phthalate, diethyl phthalate, dipentyl phthalate, and dodecyl phthalate with extremely high sensitivity in spirits without sample treatment. Among the 4 brands of spirit products, 3 kinds of PAE compounds were directly determined at very low concentrations from 1.30 to 114 ng·g -1 . Compared with other online and off-line methods, the spray-inlet microwave plasma torch tandem mass spectrometry technique is extremely simple, rapid, sensitive, and high efficient, providing an ideal screening tool for PAEs in spirits. Copyright © 2017 John Wiley & Sons, Ltd.

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

PubMed

Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

2012-11-07

Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae

PubMed Central

2012-01-01

Background Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. Results ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. Conclusions We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the

Economic viability of thin-film tandem solar modules in the United States

NASA Astrophysics Data System (ADS)

Sofia, Sarah E.; Mailoa, Jonathan P.; Weiss, Dirk N.; Stanbery, Billy J.; Buonassisi, Tonio; Peters, I. Marius

2018-05-01

Tandem solar cells are more efficient but more expensive per unit area than established single-junction (SJ) solar cells. To understand when specific tandem architectures should be utilized, we evaluate the cost-effectiveness of different II-VI-based thin-film tandem solar cells and compare them to the SJ subcells. Levelized cost of electricity (LCOE) and energy yield are calculated for four technologies: industrial cadmium telluride and copper indium gallium selenide, and their hypothetical two-terminal (series-connected subcells) and four-terminal (electrically independent subcells) tandems, assuming record SJ quality subcells. Different climatic conditions and scales (residential and utility scale) are considered. We show that, for US residential systems with current balance-of-system costs, the four-terminal tandem has the lowest LCOE because of its superior energy yield, even though it has the highest US per watt (US W-1) module cost. For utility-scale systems, the lowest LCOE architecture is the cadmium telluride single junction, the lowest US W-1 module. The two-terminal tandem requires decreased subcell absorber costs to reach competitiveness over the four-terminal one.

Demonstration of micro-projection enabled short-range communication system for 5G.

PubMed

Chou, Hsi-Hsir; Tsai, Cheng-Yu

2016-06-13

A liquid crystal on silicon (LCoS) based polarization modulated image (PMI) system architecture using red-, green- and blue-based light-emitting diodes (LEDs), which offers simultaneous micro-projection and high-speed data transmission at nearly a gigabit, serving as an alternative short-range communication (SRC) approach for personal communication device (PCD) application in 5G, is proposed and experimentally demonstrated. In order to make the proposed system architecture transparent to the future possible wireless data modulation format, baseband modulation schemes such as multilevel pulse amplitude modulation (M-PAM), M-ary phase shift keying modulation (M-PSK) and M-ary quadrature amplitude modulation (M-QAM) which can be further employed by more advanced multicarrier modulation schemes (such as DMT, OFDM and CAP) were used to investigate the highest possible data transmission rate of the proposed system architecture. The results demonstrated that an aggregative data transmission rate of 892 Mb/s and 900 Mb/s at a BER of 10^(-3) can be achieved by using 16-QAM baseband modulation scheme when data transmission were performed with and without micro-projection simultaneously.

Typing Clostridium difficile strains based on tandem repeat sequences

PubMed Central

2009-01-01

Background Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies. Results This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. Conclusion We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. PMID:19133124

Quantitative Acylcarnitine Determination by UHPLC-MS/MS – Going Beyond Tandem MS Acylcarnitine “Profiles”

PubMed Central

Minkler, Paul E.; Stoll, Maria S.K.; Ingalls, Stephen T.; Kerner, Janos; Hoppel, Charles L.

2016-01-01

Tandem MS “profiling” of acylcarnitines and amino acids was conceived as a first-tier screening method, and its application to expanded newborn screening has been enormously successful. However, unlike amino acid screening (which uses amino acid analysis as its second-tier validation of screening results), acylcarnitine “profiling” also assumed the role of second-tier validation, due to the lack of a generally accepted second-tier acylcarnitine determination method. In this report, we present results from the application of our validated UHPLC-MS/MS second-tier method for the quantification of total carnitine, free carnitine, butyrobetaine, and acylcarnitines to patient samples with known diagnoses: malonic acidemia, short-chain acyl-CoA dehydrogenase deficiency (SCADD) or isobutyryl-CoA dehydrogenase deficiency (IBD), 3-methyl-crotonyl carboxylase deficiency (3-MCC) or β-ketothiolase deficiency (BKT), and methylmalonic acidemia (MMA). We demonstrate the assay’s ability to separate constitutional isomers and diastereomeric acylcarnitines and generate values with a high level of accuracy and precision. These capabilities are unavailable when using tandem MS “profiles”. We also show examples of research interest, where separation of acylcarnitine species and accurate and precise acylcarnitine quantification is necessary. PMID:26458767

PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome

PubMed Central

Girardot, Michael; Hirasawa, Ryutaro; Kacem, Salim; Fritsch, Lauriane; Pontis, Julien; Kota, Satya K.; Filipponi, Doria; Fabbrizio, Eric; Sardet, Claude; Lohmann, Felix; Kadam, Shilpa; Ait-Si-Ali, Slimane; Feil, Robert

2014-01-01

Symmetrical dimethylation on arginine-3 of histone H4 (H4R3me2s) has been reported to occur at several repressed genes, but its specific regulation and genomic distribution remained unclear. Here, we show that the type-II protein arginine methyltransferase PRMT5 controls H4R3me2s in mouse embryonic fibroblasts (MEFs). In these differentiated cells, we find that the genome-wide pattern of H4R3me2s is highly similar to that in embryonic stem cells. In both the cell types, H4R3me2s peaks are detected predominantly at G + C-rich regions. Promoters are consistently marked by H4R3me2s, independently of transcriptional activity. Remarkably, H4R3me2s is mono-allelic at imprinting control regions (ICRs), at which it marks the same parental allele as H3K9me3, H4K20me3 and DNA methylation. These repressive chromatin modifications are regulated independently, however, since PRMT5-depletion in MEFs resulted in loss of H4R3me2s, without affecting H3K9me3, H4K20me3 or DNA methylation. Conversely, depletion of ESET (KMT1E) or SUV420H1/H2 (KMT5B/C) affected H3K9me3 and H4K20me3, respectively, without altering H4R3me2s at ICRs. Combined, our data indicate that PRMT5-mediated H4R3me2s uniquely marks the mammalian genome, mostly at G + C-rich regions, and independently from transcriptional activity or chromatin repression. Furthermore, comparative bioinformatics analyses suggest a putative role of PRMT5-mediated H4R3me2s in chromatin configuration in the nucleus. PMID:24097435

Plasmonic biosensor for label-free G-quadruplexes detection

NASA Astrophysics Data System (ADS)

Qiu, Suyan; Zhao, Fusheng; Santos, Greggy M.; Shih, Wei-Chuan

2016-03-01

G-quadruplex, readily formed by the G-rich sequence, potentially distributes in over 40 % of all human genes, such as the telomeric DNA with the G-rich sequence found at the end of the chromosome. The G-quadruplex structure is supposed to possess a diverse set of critical functions in the mammalian genome for transcriptional regulation, DNA replication and genome stability. However, most of the currently available methods for G-quadruplex identification are restricted to fluorescence techniques susceptible to poor sensitivity. It is essential to propose methods with higher sensitivity to specifically recognize the G-quadruplexes. In this study, we demonstrate a label-free plasmonic biosensor for G-quadruplex detection by relying on the advantages of nanoporous gold (NPG) disks that provide high-density plasmonic hot spots, suitable for molecular recognition capability without the requirement for labeling processes.

Solution-processed parallel tandem polymer solar cells using silver nanowires as intermediate electrode.

PubMed

Guo, Fei; Kubis, Peter; Li, Ning; Przybilla, Thomas; Matt, Gebhard; Stubhan, Tobias; Ameri, Tayebeh; Butz, Benjamin; Spiecker, Erdmann; Forberich, Karen; Brabec, Christoph J

2014-12-23

Tandem architecture is the most relevant concept to overcome the efficiency limit of single-junction photovoltaic solar cells. Series-connected tandem polymer solar cells (PSCs) have advanced rapidly during the past decade. In contrast, the development of parallel-connected tandem cells is lagging far behind due to the big challenge in establishing an efficient interlayer with high transparency and high in-plane conductivity. Here, we report all-solution fabrication of parallel tandem PSCs using silver nanowires as intermediate charge collecting electrode. Through a rational interface design, a robust interlayer is established, enabling the efficient extraction and transport of electrons from subcells. The resulting parallel tandem cells exhibit high fill factors of ∼60% and enhanced current densities which are identical to the sum of the current densities of the subcells. These results suggest that solution-processed parallel tandem configuration provides an alternative avenue toward high performance photovoltaic devices.

IgG4 related sclerosing mastitis: expanding the morphological spectrum of IgG4 related diseases.

PubMed

Chougule, Abhijit; Bal, Amanjit; Das, Ashim; Singh, Gurpreet

2015-01-01

IgG4 related disease (IgG4RD) is a recently recognised condition characterised by mass forming lesions associated with storiform fibrosis, obliterative phlebitis, lymphoplasmacytic infiltrate rich in IgG4 positive plasma cells and elevated serum IgG4 levels. Although rare, mammary involvement has been reported as IgG4 related sclerosing mastitis, the morphological counterpart of a growing family of IgG4 related diseases. A total of 17 cases belonging to mass forming benign inflammatory breast lesions such as plasma cell mastitis, granulomatous lobular mastitis, non-specific mastitis and inflammatory pseudotumour were investigated as a possible member of IgG4 related sclerosing mastitis. Clinical, radiological, histopathological and immunohistochemistry findings were noted in all cases. Cases diagnosed as inflammatory pseudotumour showed all the histopathological features of IgG4RD along with increased number of IgG4 positive plasma cells and IgG4/IgG ratio >40%. However, only a few IgG4 positive cells were seen in plasma cell mastitis, granulomatous lobular mastitis and non-specific mastitis cases. These cases also did not fulfill the morphological criteria for the diagnosis of IgG4 related diseases. IgG4RD should be excluded in plasma cell rich lesions diagnosed on core biopsies by IgG4 immunostaining. This can avoid unnecessary surgery as IgG4 related diseases respond to simple and effective steroid treatment.

Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

PubMed Central

Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

2014-01-01

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community. PMID:25148383

Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).

PubMed

Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

2014-01-01

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

Tandem Repeated Irritation Test (TRIT) Studies and Clinical Relevance: Post 2006.

PubMed

Reddy, Rasika; Maibach, Howard

2018-06-11

Single or multiple applications of irritants can lead to occupational contact dermatitis, and most commonly irritant contact dermatitis (ICD). Tandem irritation, the sequential application of two irritants to a target skin area, has been studied using the Tandem Repeated Irritation Test (TRIT) to provide a more accurate representation of skin irritation. Here we present an update to Kartono's review on tandem irritation studies since 2006 [1]. We surveyed the literature available on PubMed, Embase, Google Scholar, and the UCSF Dermatology library databases since 2006. The studies included discuss the tandem effects of common chemical irritants, organic solvents, occlusion as well as clinical relevance - and enlarge our ability to discern whether multiple chemical exposures are more or less likely to enhance irritation.

Telomeres and telomerase.

PubMed Central

Chan, Simon R W L; Blackburn, Elizabeth H

2004-01-01

Telomeres are the protective DNA-protein complexes found at the ends of eukaryotic chromosomes. Telomeric DNA consists of tandem repeats of a simple, often G-rich, sequence specified by the action of telomerase, and complete replication of telomeric DNA requires telomerase. Telomerase is a specialized cellular ribonucleoprotein reverse transcriptase. By copying a short template sequence within its intrinsic RNA moiety, telomerase synthesizes the telomeric DNA strand running 5' to 3' towards the distal end of the chromosome, thus extending it. Fusion of a telomere, either with another telomere or with a broken DNA end, generally constitutes a catastrophic event for genomic stability. Telomerase acts to prevent such fusions. The molecular consequences of telomere failure, and the molecular contributors to telomere function, with an emphasis on telomerase, are discussed here. PMID:15065663

Thermal stability of G-rich anti-parallel DNA triplexes upon insertion of LNA and α-L-LNA.

PubMed

Kosbar, Tamer R; Sofan, Mamdouh A; Abou-Zeid, Laila; Pedersen, Erik B

2015-05-14

G-rich anti-parallel DNA triplexes were modified with LNA or α-L-LNA in their Watson-Crick and TFO strands. The triplexes were formed by targeting a pyrimidine strand to a putative hairpin formed by Hoogsteen base pairing in order to use the UV melting method to evaluate the stability of the triplexes. Their thermal stability was reduced when the TFO strand was modified with LNA or α-L-LNA. The same trend was observed when the TFO strand and the purine Watson-Crick strand both were modified with LNA. When all triad components were modified with α-L-LNA and LNA in the middle of the triplex, the thermal melting was increased. When the pyrimidine sequence was modified with a single insertion of LNA or α-L-LNA the ΔTm increased. Moreover, increasing the number of α-L-LNA in the pyrimidine target sequence to six insertions, leads to a high increase in the thermal stability. The conformational S-type structure of α-L-LNA in anti-parallel triplexes is preferable for triplex stability.

ON INFRARED EXCESSES ASSOCIATED WITH Li-RICH K GIANTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rebull, Luisa M.; Carlberg, Joleen K.; Gibbs, John C.

2015-10-15

Infrared (IR) excesses around K-type red giants (RGs) have previously been discovered using Infrared Astronomy Satellite (IRAS) data, and past studies have suggested a link between RGs with overabundant Li and IR excesses, implying the ejection of circumstellar shells or disks. We revisit the question of IR excesses around RGs using higher spatial resolution IR data, primarily from the Wide-field Infrared Survey Explorer. Our goal was to elucidate the link between three unusual RG properties: fast rotation, enriched Li, and IR excess. Our sample of RGs includes those with previous IR detections, a sample with well-defined rotation and Li abundancemore » measurements with no previous IR measurements, and a large sample of RGs asserted to be Li-rich in the literature; we have 316 targets thought to be K giants, about 40% of which we take to be Li-rich. In 24 cases with previous detections of IR excess at low spatial resolution, we believe that source confusion is playing a role, in that either (a) the source that is bright in the optical is not responsible for the IR flux, or (b) there is more than one source responsible for the IR flux as measured in IRAS. We looked for IR excesses in the remaining sources, identifying 28 that have significant IR excesses by ∼20 μm (with possible excesses for 2 additional sources). There appears to be an intriguing correlation in that the largest IR excesses are all in Li-rich K giants, though very few Li-rich K giants have IR excesses (large or small). These largest IR excesses also tend to be found in the fastest rotators. There is no correlation of IR excess with the carbon isotopic ratio, {sup 12}C/{sup 13}C. IR excesses by 20 μm, though relatively rare, are at least twice as common among our sample of Li-rich K giants. If dust shell production is a common by-product of Li enrichment mechanisms, these observations suggest that the IR excess stage is very short-lived, which is supported by theoretical calculations

Predominant prevalence of human rotaviruses with the G1P[8] and G8P[8] genotypes with a short RNA profile in 2013 and 2014 in Sukhothai and Phetchaboon provinces, Thailand.

PubMed

Guntapong, Ratigorn; Tacharoenmuang, Ratana; Singchai, Phakapun; Upachai, Sompong; Sutthiwarakom, Karun; Komoto, Satoshi; Tsuji, Takao; Tharmaphornpilas, Piyanit; Yoshikawa, Tetsushi; Sangkitporn, Somchai; Taniguchi, Koki

2017-04-01

Of 2,754 stool specimens collected from children with acute gastroenteritis during 2013-2014 in Sukhothai and Phetchaboon provinces, Thailand, 666 (24.2%) were positive for rotavirus A (RVA) in polyacrylamide gel electrophoresis (PAGE). The G and P types of all RVA-positive specimens were determined by semi-nested RT-PCR. G1P[8] (56.5%) was most prevalent, followed by G2P[4] (22.1%). Unusual G8P[8] human RVAs (HuRVAs) were detected at a high frequency (20.0%). Interestingly, 171 of the 376 G1P[8] HuRVAs and all of the 133 G8P[8] HuRVAs showed a short RNA pattern in PAGE. Thus, it was shown that the properties of HuRVAs have been markedly unusual in recent years in Thailand. J. Med. Virol. 89:615-620, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Highly Efficient and Stable Sn-Rich Perovskite Solar Cells by Introducing Bromine.

PubMed

Lee, Seojun; Kang, Dong-Won

2017-07-12

Compositional engineering of recently arising methylammonium (MA) lead (Pb) halide based perovskites is an essential approach for finding better perovskite compositions to resolve still remaining issues of toxic Pb, long-term instability, etc. In this work, we carried out crystallographic, morphological, optical, and photovoltaic characterization of compositional MASn 0.6 Pb 0.4 I 3-x Br x by gradually introducing bromine (Br) into parental Pb-Sn binary perovskite (MASn 0.6 Pb 0.4 I 3 ) to elucidate its function in Sn-rich (Sn:Pb = 6:4) perovskites. We found significant advances in crystallinity and dense coverage of the perovskite films by inserting the Br into Sn-rich perovskite lattice. Furthermore, light-intensity-dependent open circuit voltage (V oc ) measurement revealed much suppressed trap-assisted recombination for a proper Br-added (x = 0.4) device. These contributed to attaining the unprecedented power conversion efficiency of 12.1% and V oc of 0.78 V, which are, to the best of our knowledge, the highest performance in the Sn-rich (≥60%) perovskite solar cells reported so far. In addition, impressive enhancement of photocurrent-output stability and little hysteresis were found, which paves the way for the development of environmentally benign (Pb reduction), stable monolithic tandem cells using the developed low band gap (1.24-1.26 eV) MASn 0.6 Pb 0.4 I 3-x Br x with suggested composition (x = 0.2-0.4).

Hematite-Rich Deposits in Capri Chasma

NASA Image and Video Library

2016-12-14

Capri Chasma is located in the eastern portion of the Valles Marineris canyon system, the largest known canyon system in the Solar System. Deeply incised canyons such as this are excellent targets for studying the Martian crust, as the walls may reveal many distinct types of bedrock. This section of the canyon was targeted by HiRISE based on a previous spectral detection of hematite-rich deposits in the area. Hematite, a common iron-oxide mineral, was first identified here by the Mars Global Surveyor Thermal Emission Spectrometer (TES). In this TES image, red pixels indicate higher abundances of hematite, while the blue and green pixels represent different types of volcanic rocks (e.g., basalt). Hematite in the Meridiani Planum region was also detected with the TES instrument (which we can see with the bright red spot on the Global TES mineral map). As a consequence, Meridiani Planum was the first landing site selected on Mars due to the spectral detection of a mineral that may have formed in the presence of liquid water. Shortly after landing, the Opportunity rover detected the presence of hematite in the form of concretions called "blueberries." The blueberries are found in association with layers of sulfate salt-rich rocks. The salts are hypothesized to have formed through the raising and lowering of the groundwater table. During one such an event, the rock altered to form the hematite-rich blueberries. As the rock was eroded away, the more resistant hematite-rich blueberries were plucked out and concentrated on the plains as a "lag" deposit. Martian blueberries are observed to be scattered across the plains of Meridiani along Opportunity's traverse from Eagle Crater to Endeavor Crater, where Opportunity continues to explore after its mission began over 10 years ago. This infrared-color image close-up highlights what is possibly the hematite-rich deposits nestled between different types of bedrock terraces in Capri Chasma. The bluish terrace is likely volcanic

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

PubMed Central

Laukkanen-Ninios, R.; Ortiz Martínez, P.; Siitonen, A.; Fredriksson-Ahomaa, M.; Korkeala, H.

2013-01-01

Sporadic and epidemiologically linked Yersinia enterocolitica strains (n = 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared. PMID:23637293

Flow field interactions between two tandem cyclists

NASA Astrophysics Data System (ADS)

Barry, Nathan; Burton, David; Sheridan, John; Thompson, Mark; Brown, Nicholas A. T.

2016-12-01

Aerodynamic drag is the primary resistive force acting on cyclists at racing speeds. Many events involve cyclists travelling in very close proximity. Previous studies have shown that interactions result in significant drag reductions for inline cyclists. However, the interaction between cyclist leg position (pedalling) and the vortical flow structures that contribute significantly to the drag on an isolated cyclist has not previously been quantified or described for tandem cyclists of varying separation. To this end, scale model cyclists were constructed for testing in a water channel for inline tandem configurations. Particle image velocimetry was used to capture time-averaged velocity fields around two tandem cyclists. Perhaps surprisingly, the wake of a trailing cyclist maintains strong similarity to the characteristic wake of a single cyclist despite a significant disturbance to the upstream flow. Together with streamwise velocity measurements through the wake and upstream of the trailing cyclist, this work supports previous findings, which showed that the trailing cyclist drag reduction is primarily due to upstream sheltering effects reducing the stagnation pressure on forward-facing surfaces.

Stacking multiple connecting functional materials in tandem organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Zhang, Tao; Wang, Deng-Ke; Jiang, Nan; Lu, Zheng-Hong

2017-02-01

Tandem device is an important architecture in fabricating high performance organic light-emitting diodes and organic photovoltaic cells. The key element in making a high performance tandem device is the connecting materials stack, which plays an important role in electric field distribution, charge generation and charge injection. For a tandem organic light-emitting diode (OLED) with a simple Liq/Al/MoO3 stack, we discovered that there is a significant current lateral spreading causing light emission over an extremely large area outside the OLED pixel when the Al thickness exceeds 2 nm. This spread light emission, caused by an inductive electric field over one of the device unit, limits one’s ability to fabricate high performance tandem devices. To resolve this issue, a new connecting materials stack with a C60 fullerene buffer layer is reported. This new structure permits optimization of the Al metal layer in the connecting stack and thus enables us to fabricate an efficient tandem OLED having a high 155.6 cd/A current efficiency and a low roll-off (or droop) in current efficiency.

Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum (cv. Heinz 1706)

PubMed Central

Krsticevic, Flavia J.; Arce, Débora P.; Ezpeleta, Joaquín; Tapia, Elizabeth

2016-01-01

In plants, fruit maturation and oxidative stress can induce small heat shock protein (sHSP) synthesis to maintain cellular homeostasis. Although the tomato reference genome was published in 2012, the actual number and functionality of sHSP genes remain unknown. Using a transcriptomic (RNA-seq) and evolutionary genomic approach, putative sHSP genes in the Solanum lycopersicum (cv. Heinz 1706) genome were investigated. A sHSP gene family of 33 members was established. Remarkably, roughly half of the members of this family can be explained by nine independent tandem duplication events that determined, evolutionarily, their functional fates. Within a mitochondrial class subfamily, only one duplicated member, Solyc08g078700, retained its ancestral chaperone function, while the others, Solyc08g078710 and Solyc08g078720, likely degenerated under neutrality and lack ancestral chaperone function. Functional conservation occurred within a cytosolic class I subfamily, whose four members, Solyc06g076570, Solyc06g076560, Solyc06g076540, and Solyc06g076520, support ∼57% of the total sHSP RNAm in the red ripe fruit. Subfunctionalization occurred within a new subfamily, whose two members, Solyc04g082720 and Solyc04g082740, show heterogeneous differential expression profiles during fruit ripening. These findings, involving the birth/death of some genes or the preferential/plastic expression of some others during fruit ripening, highlight the importance of tandem duplication events in the expansion of the sHSP gene family in the tomato genome. Despite its evolutionary diversity, the sHSP gene family in the tomato genome seems to be endowed with a core set of four homeostasis genes: Solyc05g014280, Solyc03g082420, Solyc11g020330, and Solyc06g076560, which appear to provide a baseline protection during both fruit ripening and heat shock stress in different tomato tissues. PMID:27565886

Low-Cost CdTe/Silicon Tandem Solar Cells

DOE PAGES

Tamboli, Adele C.; Bobela, David C.; Kanevce, Ana; ...

2017-09-06

Achieving higher photovoltaic efficiency in single-junction devices is becoming increasingly difficult, but tandem modules offer the possibility of significant efficiency improvements. By device modeling we show that four-terminal CdTe/Si tandem solar modules offer the prospect of 25%-30% module efficiency, and technoeconomic analysis predicts that these efficiency gains can be realized at costs per Watt that are competitive with CdTe and Si single junction alternatives. The cost per Watt of the modeled tandems is lower than crystalline silicon, but slightly higher than CdTe alone. But, these higher power modules reduce area-related balance of system costs, providing increased value especially in area-constrainedmore » applications. This avenue for high-efficiency photovoltaics enables improved performance on a near-term timeframe, as well as a path to further reduced levelized cost of electricity as module and cell processes continue to advance.« less

Low-Cost CdTe/Silicon Tandem Solar Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamboli, Adele C.; Bobela, David C.; Kanevce, Ana

Achieving higher photovoltaic efficiency in single-junction devices is becoming increasingly difficult, but tandem modules offer the possibility of significant efficiency improvements. By device modeling we show that four-terminal CdTe/Si tandem solar modules offer the prospect of 25%-30% module efficiency, and technoeconomic analysis predicts that these efficiency gains can be realized at costs per Watt that are competitive with CdTe and Si single junction alternatives. The cost per Watt of the modeled tandems is lower than crystalline silicon, but slightly higher than CdTe alone. But, these higher power modules reduce area-related balance of system costs, providing increased value especially in area-constrainedmore » applications. This avenue for high-efficiency photovoltaics enables improved performance on a near-term timeframe, as well as a path to further reduced levelized cost of electricity as module and cell processes continue to advance.« less

Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina

PubMed Central

Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

2014-01-01

Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other. PMID:25358886

Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina.

PubMed

Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

2014-10-01

To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other.

Short-Term International Internship Experiences for Future Teachers and Other Child Development Professionals

ERIC Educational Resources Information Center

Miller, Kari Knutson; Gonzalez, Amber M.

2016-01-01

This paper examines outcomes associated with participation in short-term, international internship experiences. Results suggest short-term international internship experiences contribute to rich personal and professional development outcomes. Findings highlight participant challenges associated with initial internship experiences, professional…

The direct analysis of drug distribution of rotigotine-loaded microspheres from tissue sections by LESA coupled with tandem mass spectrometry.

PubMed

Xu, Li-Xiao; Wang, Tian-Tian; Geng, Yin-Yin; Wang, Wen-Yan; Li, Yin; Duan, Xiao-Kun; Xu, Bin; Liu, Charles C; Liu, Wan-Hui

2017-09-01

The direct analysis of drug distribution of rotigotine-loaded microspheres (RoMS) from tissue sections by liquid extraction surface analysis (LESA) coupled with tandem mass spectrometry (MS/MS) was demonstrated. The RoMS distribution in rat tissues assessed by the ambient LESA-MS/MS approach without extensive or tedious sample pretreatment was compared with that obtained by a conventional liquid chromatography tandem mass spectrometry (LC-MS/MS) method in which organ excision and subsequent solvent extraction were commonly employed before analysis. Results obtained from the two were well correlated for a majority of the organs, such as muscle, liver, stomach, and hippocampus. The distribution of RoMS in the brain, however, was found to be mainly focused in the hippocampus and striatum regions as shown by the LESA-imaged profiles. The LESA approach we developed is sensitive enough, with an estimated LLOQ at 0.05 ng/mL of rotigotine in brain tissue, and information-rich with minimal sample preparation, suitable, and promising in assisting the development of new drug delivery systems for controlled drug release and protection. Graphical abstract Workflow for the LESA-MS/MS imaging of brain tissue section after intramuscular RoMS administration.

The origin and evolution of short-period Miras in the solar neighborhood: Constraints on the life cycle of old stars

NASA Astrophysics Data System (ADS)

Jura, M.

1994-02-01

The spatial distribution of the short-period (P less than 300 days) oxygen-rich Miras in the solar neighborhood can be fitted with an exponential scale height above the Galactic plane of about 600 pc. Using the Gliese catalog of local main-sequence stars, we estimate that the density of suitable G-type progenitor dwarfs within 20 pc of the Sun for these short-period Miras is 6 x 10-4/cu pc. The portion of the H-R diagram near the main-sequence turnoff of these velocity-selected Gliese stars is intermediate between that of the old open cluster NGC 188 and that of the metal-rich globular cluster, 47 Tuc. We infer that the main-sequence progenitors of the short-period Miras have masses near 1.0 solar mass, and we estimate that these Miras have ages approximately 9 x 109. We also identify a few old disk red giants in the neighborhood of the Sun. On the basis of very limited information, we estimate that the total amount of mass lost from these stars during their first ascent up the red giant branch is less than or equal to 0.1 solar mass. We derive a duration of the short-period Mira phase of close to 5 x 105 yr. This estimate for the duration of the short period Mira phase is longer than our estimate of 2 x 105 yr for the duration of the Mira phase for stars with periods longer than 300 days. From their infrared colors, we estimate a typical mass-loss rate from the short-period Miras of approximately 1 x 10-7 solar mass/yr.

Partners in crime: The role of tandem modules in gene transcription.

PubMed

Sharma, Rajal; Zhou, Ming-Ming

2015-09-01

Histones and their modifications play an important role in the regulation of gene transcription. Numerous modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and SUMOylation, have been described. These modifications almost always co-occur and thereby increase the combinatorial complexity of post-translational modification detection. The domains that recognize these histone modifications often occur in tandem in the context of larger proteins and complexes. The presence of multiple modifications can positively or negatively regulate the binding of these tandem domains, influencing downstream cellular function. Alternatively, these tandem domains can have novel functions from their independent parts. Here we summarize structural and functional information known about major tandem domains and their histone binding properties. An understanding of these interactions is key for the development of epigenetic therapy. © 2015 The Protein Society.

Fast Gas Chromatography with Tandem Mass Spectrometry Analysis of Selected Persistent Organic Pollutants and Organophosphorus and Synthetic Pyrethroid Pesticides in Indian Prawn (Fenneropenaeus indicus) in Compliance with the EU-MRLs.

PubMed

Sawant, Durvesh; Kelkar, Jitendra; Rasam, Pratap; Datar, Ajit; Hase, Prashant; Handique, Dheeraj; Bhone, Ankush; Chiplunkar, Sanket; Hate, Manish

2017-05-01

A fast GC with tandem MS method was developed and validated for multiresidue determination of 95 chemical contaminants (24 synthetic pyrethroids, 17 organochlorines, 17 organophosphorus compounds, 18 polycyclic aromatic hydrocarbons, and 19 polychlorinated biphenyls) in Indian prawns (Fenneropenaeus indicus) as per the European Union maximum residual limit requirements. Chromatographic separation and MS determination were achieved within a short run time of 18 min, without compromising sensitivity and specificity. Our findings revealed a 2.5× reduction in the run time compared with conventional GC methods. Sample preparation involved a QuEChERS-based extraction of 10 g sample with 10 mL acidified acetonitrile (1% acetic acid) and phase separation with 6 g anhydrous magnesium sulfate and 1.5 g sodium acetate. The extract was cleaned in two steps, first by dispersive cleanup with primary secondary amine and then by C18 SPE cartridge. The regression coefficients of linearity (r2) for the concentration range of 5-50 ng/mL were >0.99 for all the compounds. Recoveries at 5 and 10 ng/g levels were within the acceptable range of 70-120%. The repeatability (RSDr) and within-laboratory reproducibility (RSDwR) precisions were ≤20%. The method was successfully applied for analysis of the real world samples for incurred residues.

Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

PubMed

Kim, Yong Tae; Lee, Dohwan; Heo, Hyun Young; Sim, Jeong Eun; Woo, Kwang Man; Kim, Do Hyun; Im, Sung Gap; Seo, Tae Seok

2016-04-15

A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1 μL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthesis of neutron-rich superheavy nuclei with radioactive beams within the dinuclear system model

NASA Astrophysics Data System (ADS)

Wu, Zhi-Han; Zhu, Long; Li, Fan; Yu, Xiao-Bin; Su, Jun; Guo, Chen-Chen

2018-06-01

The production of neutron-rich superheavy nuclei with Z =105 -118 in neutron evaporation channels is investigated within the dinuclear system model. The different stable and radioactive beam-induced hot fusion reactions are studied systematically. The prospect for synthesizing neutron-rich superheavy nuclei using radioactive beams is evaluated quantitatively based on the beam intensities proposed by Argonne Tandem Linac Accelerator System [B. B. Back and C. L. Jiang, Argonne National Laboratory Report No. ANL-06/55, 2006 (unpublished)]. All possible combinations (with projectiles of Z =16 -22 and half-lives longer than 1 ms; with targets of half-lives longer than 30 days), which can be performed in available experimental equipment, for producing several unknown neutron-rich superheavy nuclei in neutron evaporation channels are investigated and the most promising reactions are predicted. It is found that the stable beams still show great advantages for producing most of superheavy nuclei. The calculated results are also compared with production cross sections in the p x n and α x n evaporation channels [Hong et al., Phys. Lett. B 764, 42 (2017), 10.1016/j.physletb.2016.11.002]. We find that the radioactive beam-induced reactions are comparable to the stable beam-induced reactions in charged particle evaporation channels. To obtain more experimental achievements, the beam intensities of modern radioactive beam facilities need to be further improved in the future.

GSK3β phosphorylates newly identified site in the proline-alanine-rich region of cardiac myosin-binding protein C and alters cross-bridge cycling kinetics in human: short communication.

PubMed

Kuster, Diederik W D; Sequeira, Vasco; Najafi, Aref; Boontje, Nicky M; Wijnker, Paul J M; Witjas-Paalberends, E Rosalie; Marston, Steven B; Dos Remedios, Cristobal G; Carrier, Lucie; Demmers, Jeroen A A; Redwood, Charles; Sadayappan, Sakthivel; van der Velden, Jolanda

2013-02-15

Cardiac myosin-binding protein C (cMyBP-C) regulates cross-bridge cycling kinetics and, thereby, fine-tunes the rate of cardiac muscle contraction and relaxation. Its effects on cardiac kinetics are modified by phosphorylation. Three phosphorylation sites (Ser275, Ser284, and Ser304) have been identified in vivo, all located in the cardiac-specific M-domain of cMyBP-C. However, recent work has shown that up to 4 phosphate groups are present in human cMyBP-C. To identify and characterize additional phosphorylation sites in human cMyBP-C. Cardiac MyBP-C was semipurified from human heart tissue. Tandem mass spectrometry analysis identified a novel phosphorylation site on serine 133 in the proline-alanine-rich linker sequence between the C0 and C1 domains of cMyBP-C. Unlike the known sites, Ser133 was not a target of protein kinase A. In silico kinase prediction revealed glycogen synthase kinase 3β (GSK3β) as the most likely kinase to phosphorylate Ser133. In vitro incubation of the C0C2 fragment of cMyBP-C with GSK3β showed phosphorylation on Ser133. In addition, GSK3β phosphorylated Ser304, although the degree of phosphorylation was less compared with protein kinase A-induced phosphorylation at Ser304. GSK3β treatment of single membrane-permeabilized human cardiomyocytes significantly enhanced the maximal rate of tension redevelopment. GSK3β phosphorylates cMyBP-C on a novel site, which is positioned in the proline-alanine-rich region and increases kinetics of force development, suggesting a noncanonical role for GSK3β at the sarcomere level. Phosphorylation of Ser133 in the linker domain of cMyBP-C may be a novel mechanism to regulate sarcomere kinetics.

Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China

PubMed Central

SHI, YUNFANG; LI, XIAOZHOU; JU, DUAN; LI, YAN; ZHANG, XIULING; ZHANG, YING

2015-01-01

Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24–48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome. PMID:26622392

Greater enrichment of triacylglycerol-rich lipoproteins with apolipoproteins E and C-III after meals rich in saturated fatty acids than after meals rich in unsaturated fatty acids.

PubMed

Jackson, Kim G; Wolstencroft, Emma J; Bateman, Paul A; Yaqoob, Parveen; Williams, Christine M

2005-01-01

Although there is considerable interest in the postprandial events involved in the absorption of dietary fats and the subsequent metabolism of diet-derived triacylglycerol-rich lipoproteins, little is known about the effects of meal fatty acids on the composition of these particles. We examined the effect of meal fatty acids on the lipid and apolipoprotein contents of triacylglycerol-rich lipoproteins. Ten normolipidemic men received in random order a mixed meal containing 50 g of a mixture of palm oil and cocoa butter [rich in saturated fatty acids (SFAs)], safflower oil [n-6 polyunsaturated fatty acids (PUFAs)], or olive oil [monounsaturated fatty acids (MUFAs)] on 3 occasions. Fasting and postprandial apolipoproteins B-48, B-100, E, C-II, and C-III and lipids (triacylglycerol and cholesterol) were measured in plasma fractions with Svedberg flotation rates (S(f)) >400, S(f) 60-400, and S(f) 20-60. Calculation of the composition of the triacylglycerol-rich lipoproteins (expressed per mole of apolipoprotein B) showed notable differences in the lipid and apolipoprotein contents of the SFA-enriched particles in the S(f) > 400 and S(f) 60-400 fractions. After the SFA meal, triacylglycerol-rich lipoproteins in these fractions showed significantly greater amounts of triacylglycerol and of apolipoproteins C-II (S(f) 60-400 fraction only), C-III, and E than were found after the MUFA meal (P < 0.02) and more cholesterol, apolipoprotein C-III (S(f) > 400 fraction only), and apolipoprotein E than after the PUFA meal (P < 0.02). Differences in the composition of S(f) > 400 and S(f) 60-400 triacylglycerol-rich lipoproteins formed after saturated compared with unsaturated fatty acid-rich meals may explain differences in the metabolic handling of dietary fats.

The effect of dietary supplementation of algae rich in docosahexaenoic acid on boar fertility.

PubMed

Murphy, E M; Stanton, C; Brien, C O '; Murphy, C; Holden, S; Murphy, R P; Varley, P; Boland, M P; Fair, S

2017-03-01

The objective of this study was to assess the effects of dietary supplementation of a commercial algal product rich in docosahexaenoic acid (DHA) on boar fertility as assessed in vitro and in vivo. Boars were fed one of three experimental diets for 19 weeks: (i) Control (Ctl) diet (n = 31), (ii) Ctl diet plus 75g All-G-Rich per day (n = 31) or (iii) Ctl diet plus 150g All-G-Rich per day (n = 30). Parameters assessed were (i) raw semen quality; volume, sperm concentration, total motility and morphology (ii) liquid semen quality; progressive motility, viability, hypotonic resistance and acrosomal integrity (iii) frozen-thawed semen quality; motility, thermal stress, viability, membrane fluidity and mitochondrial activity (iv) sperm and seminal plasma (SP) fatty acid composition (FAC) (v) total antioxidant capacity (TAC) of SP and (vi) farrowing rates and litter sizes of sows (n = 1158) inseminated with liquid semen. Boars consuming 75g All-G-Rich had a larger semen volume (P < 0.05) and a higher total sperm number (P < 0.01) than the Ctl treatment, however, there was no effect of treatment on any other semen quality parameter (P > 0.05). There was no effect of dietary treatment on the FAC and TAC of SP or on farrowing rate and litter size (P > 0.05). There was an effect of dietary treatment on the FAC of sperm, represented by an 1.72 and 1.60 fold increase in the DHA content for 75 and 150g treatments, respectively, compared to the Ctl treatment. In conclusion, a significant increase in semen volume and total sperm number in boars supplemented 75g All-G-Rich daily, resulted in an increase in production of 3 to 4 more doses per ejaculate, thus, indicating that the feeding regime described within this study has the potential for increasing the output of boar studs. Copyright © 2016 Elsevier Inc. All rights reserved.

Tumor microenvironment: Modulation by decorin and related molecules harboring leucine-rich tandem motifs.

PubMed

Goldoni, Silvia; Iozzo, Renato V

2008-12-01

Decorin, the prototype member of the small leucine-rich proteoglycans, resides in the tumor microenvironment and affects the biology of various types of cancer by downregulating the activity of several receptors involved in cell growth and survival. Decorin binds to and modulates the signaling of the epidermal growth factor receptor and other members of the ErbB family of receptor tyrosine kinases. It exerts its antitumor activity by a dual mechanism: via inhibition of these key receptors through their physical downregulation coupled with attenuation of their signaling, and by binding to and sequestering TGFbeta. Decorin also modulates the insulin-like growth factor receptor and the low-density lipoprotein receptor-related protein 1, which indirectly affects the TGFbeta receptor pathway. When expressed in tumor xenograft-bearing mice or injected systemically, decorin inhibits both primary tumor growth and metastatic spreading. In this review, we summarize the latest reports on decorin and related molecules that are relevant to cancer and bring forward the idea of decorin as an anticancer therapeutic and possible prognostic marker for patients affected by various types of tumors. We also discuss the role of lumican and LRIG1, a novel cell growth inhibitor homologous to decorin. (c) 2008 Wiley-Liss, Inc.

Determination of phosphatidylethanolamine molecular species in various food matrices by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2).

PubMed

Zhou, Li; Zhao, Minjie; Ennahar, Saïd; Bindler, Françoise; Marchioni, Eric

2012-04-01

A liquid chromatographic-electrospray ionization-tandem mass spectrometric (LC-ESI-MS(2)) method has been developed for determination of the molecular species of phosphatidylethanolamine (PE) in four food matrices (soy, egg yolk, ox liver, and krill oil). The extraction and purification method consisted of a pressurized liquid extraction procedure for total lipid (TL) extraction, purification of phospholipids (PLs) by adsorption on a silica gel column, and separation of PL classes by semi-preparative normal-phase HPLC. Separation and identification of PE molecular species were performed by reversed-phase HPLC coupled with electrospray ionization tandem mass spectrometry (ESI-MS(2)). Methanol containing 5 mmol L(-1) ammonium formate was used as the mobile phase. A variety of PE molecular species were detected in the four food matrices. (C16:0-C18:2)PE, (C18:2-C18:2)PE, and (C16:0-C18:1)PE were the major PE molecular species in soy. Egg yolk PE contained (C16:0-C18:1)PE, (C18:0-C18:1)PE, (C18:0-C18:2)PE, and (C16:0-C18:2)PE as the major molecular species. Ox liver PE was rich in the species (C18:0-C18:1)PE, (C18:0-C20:4)PE, and (C18:0-C18:2)PE. Finally, krill oil which was particularly rich in (C16:0(alkyl)-C22:6(acyl))plasmanylethanolamine (PakE), (C16:0-C22:6)PE, and (C16:0-C20:5)PE, seemed to be an interesting potential source for supplementation of food with eicosapentaenoic acid and docosahexaenoic acid.

Rich-club organization of the newborn human brain

PubMed Central

Ball, Gareth; Aljabar, Paul; Zebari, Sally; Tusor, Nora; Arichi, Tomoki; Merchant, Nazakat; Robinson, Emma C.; Ogundipe, Enitan; Rueckert, Daniel; Edwards, A. David; Counsell, Serena J.

2014-01-01

Combining diffusion magnetic resonance imaging and network analysis in the adult human brain has identified a set of highly connected cortical hubs that form a “rich club”—a high-cost, high-capacity backbone thought to enable efficient network communication. Rich-club architecture appears to be a persistent feature of the mature mammalian brain, but it is not known when this structure emerges during human development. In this longitudinal study we chart the emergence of structural organization in mid to late gestation. We demonstrate that a rich club of interconnected cortical hubs is already present by 30 wk gestation. Subsequently, until the time of normal birth, the principal development is a proliferation of connections between core hubs and the rest of the brain. We also consider the impact of environmental factors on early network development, and compare term-born neonates to preterm infants at term-equivalent age. Though rich-club organization remains intact following premature birth, we reveal significant disruptions in both in cortical–subcortical connectivity and short-distance corticocortical connections. Rich club organization is present well before the normal time of birth and may provide the fundamental structural architecture for the subsequent emergence of complex neurological functions. Premature exposure to the extrauterine environment is associated with altered network architecture and reduced network capacity, which may in part account for the high prevalence of cognitive problems in preterm infants. PMID:24799693

Altered Methylation in Tandem Repeat Element and Elemental Component Levels in Inhalable Air Particles

PubMed Central

Hou, Lifang; Zhang, Xiao; Zheng, Yinan; Wang, Sheng; Dou, Chang; Guo, Liqiong; Byun, Hyang-Min; Motta, Valeria; McCracken, John; Díaz, Anaité; Kang, Choong-Min; Koutrakis, Petros; Bertazzi, Pier Alberto; Li, Jingyun; Schwartz, Joel; Baccarelli, Andrea A.

2014-01-01

Exposure to particulate matter (PM) has been associated with lung cancer risk in epidemiology investigations. Elemental components of PM have been suggested to have critical roles in PM toxicity, but the molecular mechanisms underlying their association with cancer risks remain poorly understood. DNA methylation has emerged as a promising biomarker for environmental-related diseases, including lung cancer. In this study, we evaluated the effects of PM elemental components on methylation of three tandem repeats in a highly-exposed population in Beijing, China. The Beijing Truck Driver Air Pollution Study was conducted shortly before the 2008 Beijing Olympic Games (June 15-July 27, 2008) and included 60 truck drivers and 60 office workers. On two days separated by 1-2 weeks, we measured blood DNA methylation of SATα, NBL2, D4Z4, and personal exposure to eight elemental components in PM2.5, including aluminum (Al), silicon (Si), sulfur (S), potassium (K), calcium (Ca) titanium (Ti), iron (Fe), and zinc (Zn). We estimated the associations of individual elemental component with each tandem repeat methylation in generalized estimating equations (GEE) models adjusted for PM2.5 mass and other covariates. Out of the eight examined elements, NBL2 methylation was positively associated with concentrations of Si (0.121, 95%CI: 0.030; 0.212, FDR=0.047) and Ca (0.065, 95%CI: 0.014; 0.115, FDR=0.047) in truck drivers. In office workers, SATα methylation was positively associated with concentrations of S (0.115, 95%CI: 0.034; 0.196, FDR=0.042). PM-associated differences in blood tandem-repeat methylation may help detect biological effects of the exposure and identify individuals who may eventually experience higher lung cancer risk. PMID:24273195

Perovskite-perovskite tandem photovoltaics with optimized band gaps

NASA Astrophysics Data System (ADS)

Eperon, Giles E.; Leijtens, Tomas; Bush, Kevin A.; Prasanna, Rohit; Green, Thomas; Wang, Jacob Tse-Wei; McMeekin, David P.; Volonakis, George; Milot, Rebecca L.; May, Richard; Palmstrom, Axel; Slotcavage, Daniel J.; Belisle, Rebecca A.; Patel, Jay B.; Parrott, Elizabeth S.; Sutton, Rebecca J.; Ma, Wen; Moghadam, Farhad; Conings, Bert; Babayigit, Aslihan; Boyen, Hans-Gerd; Bent, Stacey; Giustino, Feliciano; Herz, Laura M.; Johnston, Michael B.; McGehee, Michael D.; Snaith, Henry J.

2016-11-01

We demonstrate four- and two-terminal perovskite-perovskite tandem solar cells with ideally matched band gaps. We develop an infrared-absorbing 1.2-electron volt band-gap perovskite, FA0.75Cs0.25Sn0.5Pb0.5I3, that can deliver 14.8% efficiency. By combining this material with a wider-band gap FA0.83Cs0.17Pb(I0.5Br0.5)3 material, we achieve monolithic two-terminal tandem efficiencies of 17.0% with >1.65-volt open-circuit voltage. We also make mechanically stacked four-terminal tandem cells and obtain 20.3% efficiency. Notably, we find that our infrared-absorbing perovskite cells exhibit excellent thermal and atmospheric stability, not previously achieved for Sn-based perovskites. This device architecture and materials set will enable “all-perovskite” thin-film solar cells to reach the highest efficiencies in the long term at the lowest costs.

Stacking multiple connecting functional materials in tandem organic light-emitting diodes

PubMed Central

Zhang, Tao; Wang, Deng-Ke; Jiang, Nan; Lu, Zheng-Hong

2017-01-01

Tandem device is an important architecture in fabricating high performance organic light-emitting diodes and organic photovoltaic cells. The key element in making a high performance tandem device is the connecting materials stack, which plays an important role in electric field distribution, charge generation and charge injection. For a tandem organic light-emitting diode (OLED) with a simple Liq/Al/MoO3 stack, we discovered that there is a significant current lateral spreading causing light emission over an extremely large area outside the OLED pixel when the Al thickness exceeds 2 nm. This spread light emission, caused by an inductive electric field over one of the device unit, limits one’s ability to fabricate high performance tandem devices. To resolve this issue, a new connecting materials stack with a C60 fullerene buffer layer is reported. This new structure permits optimization of the Al metal layer in the connecting stack and thus enables us to fabricate an efficient tandem OLED having a high 155.6 cd/A current efficiency and a low roll-off (or droop) in current efficiency. PMID:28225028

Multiple functions of the leucine-rich repeat protein LrrA of Treponema denticola.

PubMed

Ikegami, Akihiko; Honma, Kiyonobu; Sharma, Ashu; Kuramitsu, Howard K

2004-08-01

The gene lrrA, encoding a leucine-rich repeat protein, LrrA, that contains eight consensus tandem repeats of 23 amino acid residues, has been identified in Treponema denticola ATCC 35405. A leucine-rich repeat is a generally useful protein-binding motif, and proteins containing this repeat are typically involved in protein-protein interactions. Southern blot analysis demonstrated that T. denticola ATCC 35405 expresses the lrrA gene, but the gene was not identified in T. denticola ATCC 33520. In order to analyze the functions of LrrA in T. denticola, an lrrA-inactivated mutant of strain ATCC 35405 and an lrrA gene expression transformant of strain ATCC 33520 were constructed. Characterization of the mutant and transformant demonstrated that LrrA is associated with the extracytoplasmic fraction of T. denticola and expresses multifunctional properties. It was demonstrated that the attachment of strain ATCC 35405 to HEp-2 cell cultures and coaggregation with Tannerella forsythensis were attenuated by the lrrA mutation. In addition, an in vitro binding assay demonstrated specific binding of LrrA to a portion of the Tannerella forsythensis leucine-rich repeat protein, BspA, which is mediated by the N-terminal region of LrrA. It was also observed that the lrrA mutation caused a reduction of swarming in T. denticola ATCC 35405 and consequently attenuated tissue penetration. These results suggest that the leucine-rich repeat protein LrrA plays a role in the attachment and penetration of human epithelial cells and coaggregation with Tannerella forsythensis. These properties may play important roles in the virulence of T. denticola.

Electrical and optical analyses of tandem organic light-emitting diodes with organic charge-generation layer

NASA Astrophysics Data System (ADS)

Kim, Bong Sung; Chae, Heeyeop; Chung, Ho Kyoon; Cho, Sung Min

2018-06-01

The electrical and optical properties of tandem organic light-emitting diodes (OLEDs), in which a fluorescent and phosphorescent emitting units are connected by an organic charge-generation layer (CGL), were experimentally analyzed. To investigate the internal properties of the tandem OLEDs, we fabricated and compared two single, two homo-tandem, and two hetero-tandem OLEDs using the fluorescent and phosphorescent units. From the experimental results of the OLEDs obtained at the same current density, the voltage across the CGL as well as the individual emission spectra and luminance of each unit of tandem OLEDs were obtained and compared with the theoretical simulation results. The analysis method proposed in this study can be utilized as a method to verify the accuracy of optical or electrical computer simulation of tandem OLED and it will be useful to understand the overall electrical and optical characteristics of tandem OLEDs.

Kinetic, mechanistic, and structural modeling studies of truncated wild-type leucine-rich repeat kinase 2 and the G2019S mutant.

PubMed

Liu, Min; Kang, Stephanie; Ray, Soumya; Jackson, Justin; Zaitsev, Alexandra D; Gerber, Scott A; Cuny, Gregory D; Glicksman, Marcie A

2011-11-01

Leucine-rich repeat kinase 2 (LRRK2), a large and complex protein that possesses two enzymatic properties, kinase and GTPase, is one of the major genetic factors in Parkinson's disease (PD). Here, we characterize the kinetic and catalytic mechanisms of truncated wild-type (t-wt) LRRK2 and its most common mutant, G2019S (t-G2019S), with a structural interpretation of the kinase domain. First, the substitution of threonine with serine in the LRRKtide peptide results in a much less efficient substrate as demonstrated by a 26-fold decrease in k(cat) and a 6-fold decrease in binding affinity. The significant decrease in k(cat) is attributed to a slow chemical transfer step as evidenced by the inverse solvent kinetic isotope effect in the proton inventory and pL (pH or pD)-dependent studies. The shape of the proton inventory and pL profile clearly signals the involvement of a general base (pK(a) = 7.5) in the catalysis with a low fractionation factor in the ground state. We report for the first time that the increased kinase activity of the G2019S mutant is substrate-dependent. Homology modeling of the kinase domain (open and closed forms) and structural analysis of the docked peptide substrates suggest that electrostatic interactions play an important role in substrate recognition, which is affected by G2019S and may directly influence the kinetic properties of the enzyme. Finally, the GTPase activity of the t-G2019S mutant was characterized, and the mutation modestly decreases GTPase activity without significantly affecting GTP binding affinity.

Importance of fingering convection for accreting white dwarfs in the framework of full evolutionary calculations: the case of the hydrogen-rich white dwarfs GD 133 and G 29-38

NASA Astrophysics Data System (ADS)

Wachlin, F. C.; Vauclair, G.; Vauclair, S.; Althaus, L. G.

2017-05-01

Context. A large fraction of white dwarfs show photospheric chemical composition that is polluted by heavy elements accreted from a debris disk. Such debris disks result from the tidal disruption of rocky planetesimals that have survived to whole stellar evolution from the main sequence to the final white dwarf stage. Determining the accretion rate of this material is an important step toward estimating the mass of the planetesimals and understanding the ultimate fate of the planetary systems. Aims: The accretion of heavy material with a mean molecular weight, μ, higher than the mean molecular weight of the white dwarf outer layers, induces a double-diffusive instability producing the fingering convection and an extra-mixing. As a result, the accreted material is diluted deep into the star. We explore the effect of this extra-mixing on the abundance evolution of Mg, O, Ca, Fe and Si in the cases of the two well-studied polluted DAZ white dwarfs: GD 133 and G 29-38. Methods: We performed numerical simulations of the accretion of material that has a chemical composition similar to the bulk Earth composition. We assumed a continuous and uniform accretion and considered a range of accretion rates from 104 g/s to 1010 g/s. Two cases are simulated, one using the standard mixing length theory (MLT) and one including the double-diffusive instability (fingering convection). Results: The double-diffusive instability develops on a very short timescale. The surface abundance rapidly reaches a stationary value while the depth of the zone mixed by the fingering convection increases. In the case of GD 133, the accretion rate needed to reproduce the observed abundances exceeds by more than two orders of magnitude the rate estimated by neglecting the fingering convection. In the case of G 29-38 the needed accretion rate is increased by approximately 1.7 dex. Conclusions: Our numerical simulations of the accretion of heavy elements on the hydrogen-rich white dwarf GD 133 and G 29

Use of rich-media resources by engineering undergraduates

NASA Astrophysics Data System (ADS)

Gillie, Martin; Dahli, Ranim; Saunders, Fiona C.; Gibson, Andrew

2017-11-01

The ability to develop and distribute digital teaching resources in higher education has developed rapidly over the last decade but research into how students use such resources has received limited attention. This study uses questionnaire results, Internet analytic data and semi-structured interviews to examine the use of three types of rich-media teaching resources - lecture podcasts, key-concept videos and tutorial solution videos - by engineering undergraduates. It is found that students value all three types of resource, especially for revision and as a supplement to lectures. Students find short, focused resources more useful than longer ones. Non-native English speakers and those with disabilities derive particular benefits from the resources. The effect of rich-media resources on lecture attendance is found to be small, and two-way.

TandEM: Titan and Enceladus mission

USGS Publications Warehouse

Coustenis, A.; Atreya, S.K.; Balint, T.; Brown, R.H.; Dougherty, M.K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R.A.; Griffith, C.A.; Gurvits, L.I.; Jaumann, R.; Langevin, Y.; Leese, M.R.; Lunine, J.I.; McKay, C.P.; Moussas, X.; Muller-Wodarg, I.; Neubauer, F.; Owen, T.C.; Raulin, F.; Sittler, E.C.; Sohl, F.; Sotin, Christophe; Tobie, G.; Tokano, T.; Turtle, E.P.; Wahlund, J.-E.; Waite, J.H.; Baines, K.H.; Blamont, J.; Coates, A.J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R.D.; Morse, A.; Porco, C.C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J.C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D.H.; Benilan, Y.; Bertucci, C.; Bezard, B.; Bjoraker, G.L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M.T.; Chassefiere, E.; Coll, P.; Combes, M.; Cooper, J.F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I.A.; de Angelis, E.; De Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F.M.; Fortes, A.D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Kuppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le, Mouelic S.; Lebonnois, S.; Ledvina, S.; Li, Ji; Livengood, T.A.; Lopes, R.M.; Lopez-Moreno, J. -J.; Luz, D.; Mahaffy, P.R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Salvan, C.M.; Milillo, A.; Mitchell, D.G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, Catherine D.; Nixon, C.A.; Mvondo, D.N.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F.T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Bermejo, M.R.; Sarris, E.T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L.J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D.F.; Szego, K.; Szopa,

2009-01-01

TandEM was proposed as an L-class (large) mission in response to ESA’s Cosmic Vision 2015–2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini–Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini–Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfière) and possibly several landing probes to be delivered through the atmosphere.

TandEM: Titan and Enceladus mission

NASA Astrophysics Data System (ADS)

Coustenis, A.; Atreya, S. K.; Balint, T.; Brown, R. H.; Dougherty, M. K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R. A.; Griffith, C. A.; Gurvits, L. I.; Jaumann, R.; Langevin, Y.; Leese, M. R.; Lunine, J. I.; McKay, C. P.; Moussas, X.; Müller-Wodarg, I.; Neubauer, F.; Owen, T. C.; Raulin, F.; Sittler, E. C.; Sohl, F.; Sotin, C.; Tobie, G.; Tokano, T.; Turtle, E. P.; Wahlund, J.-E.; Waite, J. H.; Baines, K. H.; Blamont, J.; Coates, A. J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R. D.; Morse, A.; Porco, C. C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J. C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D. H.; Bénilan, Y.; Bertucci, C.; Bézard, B.; Bjoraker, G. L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M. T.; Chassefière, E.; Coll, P.; Combes, M.; Cooper, J. F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I. A.; de Angelis, E.; de Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F. M.; Fortes, A. D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Küppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le Mouélic, S.; Lebonnois, S.; Ledvina, S.; Li, J.; Livengood, T. A.; Lopes, R. M.; Lopez-Moreno, J.-J.; Luz, D.; Mahaffy, P. R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Menor Salvan, C.; Milillo, A.; Mitchell, D. G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, C. D.; Nixon, C. A.; Nna Mvondo, D.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F. T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Ruiz Bermejo, M.; Sarris, E. T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L. J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D. F.; Szego, K.; Szopa, C.; Thissen, R.; Tomasko, M. G.; Toublanc, D.; Vali, H.; Vardavas, I.; Vuitton, V.; West, R. A.; Yelle, R.; Young, E. F.

2009-03-01

TandEM was proposed as an L-class (large) mission in response to ESA’s Cosmic Vision 2015-2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini-Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini-Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfière) and possibly several landing probes to be delivered through the atmosphere.

Short-range test of the universality of gravitational constant G at the millimeter scale using a digital image sensor

NASA Astrophysics Data System (ADS)

Ninomiya, K.; Akiyama, T.; Hata, M.; Hatori, M.; Iguri, T.; Ikeda, Y.; Inaba, S.; Kawamura, H.; Kishi, R.; Murakami, H.; Nakaya, Y.; Nishio, H.; Ogawa, N.; Onishi, J.; Saiba, S.; Sakuta, T.; Tanaka, S.; Tanuma, R.; Totsuka, Y.; Tsutsui, R.; Watanabe, K.; Murata, J.

2017-09-01

The composition dependence of gravitational constant G is measured at the millimeter scale to test the weak equivalence principle, which may be violated at short range through new Yukawa interactions such as the dilaton exchange force. A torsion balance on a turning table with two identical tungsten targets surrounded by two different attractor materials (copper and aluminum) is used to measure gravitational torque by means of digital measurements of a position sensor. Values of the ratios \\tilde{G}_Al-W/\\tilde{G}_Cu-W -1 and \\tilde{G}_Cu-W/GN -1 were (0.9 +/- 1.1sta +/- 4.8sys) × 10-2 and (0.2 +/- 0.9sta +/- 2.1sys) × 10-2 , respectively; these were obtained at a center to center separation of 1.7 cm and surface to surface separation of 4.5 mm between target and attractor, which is consistent with the universality of G. A weak equivalence principle (WEP) violation parameter of η_Al-Cu(r∼ 1 cm)=(0.9 +/- 1.1sta +/- 4.9sys) × 10-2 at the shortest range of around 1 cm was also obtained.

Black manganese-rich crusts on a Gothic cathedral

NASA Astrophysics Data System (ADS)

Macholdt, Dorothea S.; Herrmann, Siegfried; Jochum, Klaus Peter; Kilcoyne, A. L. David; Laubscher, Thomas; Pfisterer, Jonas H. K.; Pöhlker, Christopher; Schwager, Beate; Weber, Bettina; Weigand, Markus; Domke, Katrin F.; Andreae, Meinrat O.

2017-12-01

Black manganese-rich crusts are found worldwide on the façades of historical buildings. In this study, they were studied exemplarily on the façade of the Freiburger Münster (Freiburg Minster), Germany, and measured in-situ by portable X-ray fluorescence (XRF). The XRF was calibrated to allow the conversion from apparent mass fractions to Mn surface density (Mn mass per area), to compensate for the fact that portable XRF mass fraction measurements from thin layers violate the assumption of a homogeneous measurement volume. Additionally, 200-nm femtosecond laser ablation-inductively coupled plasma-mass spectrometry (fs LA-ICP-MS) measurements, scanning transmission X-ray microscopy-near edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS), Raman spectroscopy, and imaging by light microscopy were conducted to obtain further insight into the crust material, such as potential biogenic contributions, element distributions, trace element compositions, and organic functional groups. While black crusts of various types are present at many places on the minster's facade, crusts rich in Mn (with a Mn surface density >150 μg cm-2) are restricted to a maximum height of about 7 m. The only exceptions are those developed on the Renaissance-Vorhalle (Renaissance Portico) at a height of about 8 m. This part of the façade had been cleaned and treated with a silicon resin as recently as 2003. These crusts thus accumulated over a period of only 12 years. Yet, they are exceptionally Mn-rich with a surface density of 1200 μg cm-2, and therefore require an accumulation rate of about 100 μg cm-2 Mn per year. Trace element analyses support the theory that vehicle emissions are responsible for most of the Mn supply. Lead, barium, and zinc correlate with manganese, indicating that tire material, brake pads, and resuspended road dust are likely to be the element sources. Microscopic investigations show no organisms on or in the Mn-rich crusts. In contrast, Mn-free black

Tandem microwave waste remediation and decontamination system

DOEpatents

Wicks, George G.; Clark, David E.; Schulz, Rebecca L.

1999-01-01

The invention discloses a tandem microwave system consisting of a primary chamber in which microwave energy is used for the controlled combustion of materials. A second chamber is used to further treat the off-gases from the primary chamber by passage through a susceptor matrix subjected to additional microwave energy. The direct microwave radiation and elevated temperatures provide for significant reductions in the qualitative and quantitative emissions of the treated off gases. The tandem microwave system can be utilized for disinfecting wastes, sterilizing materials, and/or modifying the form of wastes to solidify organic or inorganic materials. The simple design allows on-site treatment of waste by small volume waste generators.

Optimizing a tandem disk model

NASA Astrophysics Data System (ADS)

Healey, J. V.

1983-08-01

The optimum values of the solidity ratio, tip speed ratio (TSR), and the preset angle of attack, the corresponding distribution, and the breakdown mechanism for a tandem disk model for a crosswind machine such as a Darrieus are examined analytically. Equations are formulated for thin blades with zero drag in consideration of two plane rectangular disks, both perpendicular to the wind flow. Power coefficients are obtained for both disks and comparisons are made between a single-disk system and a two-disk system. The power coefficient for the tandem disk model is shown to be a sum of the coefficients of the individual disks, with a maximum value of twice the Betz limit at an angle of attack of -1 deg and the TSR between 4-7. The model, applied to the NACA 0012 profile, gives a maximum power coefficient of 0.967 with a solidity ratio of 0.275 and highly limited ranges for the angle of attack and TSR.

Investigation of natural phosphatidylcholine sources: separation and identification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2) of molecular species.

PubMed

Le Grandois, Julie; Marchioni, Eric; Zhao, Minjie; Giuffrida, Francesca; Ennahar, Saïd; Bindler, Françoise

2009-07-22

This study is a contribution to the exploration of natural phospholipid (PL) sources rich in long-chain polyunsaturated fatty acids (LC-PUFAs) with nutritional interest. Phosphatidylcholines (PCs) were purified from total lipid extracts of different food matrices, and their molecular species were separated and identified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(2)). Fragmentation of lithiated adducts allowed for the identification of fatty acids linked to the glycerol backbone. Soy PC was particularly rich in species containing essential fatty acids, such as (18:2-18:2)PC (34.0%), (16:0-18:2)PC (20.8%), and (18:1-18:2)PC (16.3%). PC from animal sources (ox liver and egg yolk) contained major molecular species, such as (16:0-18:2)PC, (16:0-18:1)PC, (18:0-18:2)PC, or (18:0-18:1)PC. Finally, marine source (krill oil), which was particularly rich in (16:0-20:5)PC and (16:0-22:6)PC, appeared to be an interesting potential source for food supplementation with LC-PUFA-PLs, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).

Rapid determination of phenolic compounds and alkaloids of carob flour by improved liquid chromatography tandem mass spectrometry.

PubMed

Ortega, Nàdia; Macià, Alba; Romero, Maria-Paz; Trullols, Esther; Morello, Jose-Ramón; Anglès, Neus; Motilva, Maria-Jose

2009-08-26

An improved chromatographic method was developed using ultra-performance liquid chromatography-tandem mass spectrometry to identify and quantify phenolic compounds and alkaloids, theobromine and caffeine, in carob flour samples. The developed method has been validated in terms of speed, sensitivity, selectivity, peak efficiency, linearity, reproducibility, limits of detection, and limits of quantification. The chromatographic method allows the identification and quantification of 20 phenolic compounds, that is, phenolic acids, flavonoids, and their aglycone and glucoside forms, together with the determination of the alkaloids, caffeine and theobromine, at low concentration levels all in a short analysis time of less than 20 min.

Dynamics of tandem bubble interaction in a microfluidic channel

PubMed Central

Yuan, Fang; Sankin, Georgy; Zhong, Pei

2011-01-01

The dynamics of tandem bubble interaction in a microfluidic channel (800 × 21 μm, W × H) have been investigated using high-speed photography, with resultant fluid motion characterized by particle imaging velocimetry. A single or tandem bubble is produced reliably via laser absorption by micron-sized gold dots (6 μm in diameter with 40 μm in separation distance) coated on a glass surface of the microfluidic channel. Using two pulsed Nd:YAG lasers at λ = 1064 nm and ∼10 μJ/pulse, the dynamics of tandem bubble interaction (individual maximum bubble diameter of 50 μm with a corresponding collapse time of 5.7 μs) are examined at different phase delays. In close proximity (i.e., interbubble distance = 40 μm or γ = 0.8), the tandem bubbles interact strongly with each other, leading to asymmetric deformation of the bubble walls and jet formation, as well as the production of two pairs of vortices in the surrounding fluid rotating in opposite directions. The direction and speed of the jet (up to 95 m/s), as well as the orientation and strength of the vortices can be varied by adjusting the phase delay. PMID:22088007

Dynamics of tandem bubble interaction in a microfluidic channel.

PubMed

Yuan, Fang; Sankin, Georgy; Zhong, Pei

2011-11-01

The dynamics of tandem bubble interaction in a microfluidic channel (800  ×  21 μm, W × H) have been investigated using high-speed photography, with resultant fluid motion characterized by particle imaging velocimetry. A single or tandem bubble is produced reliably via laser absorption by micron-sized gold dots (6 μm in diameter with 40 μm in separation distance) coated on a glass surface of the microfluidic channel. Using two pulsed Nd:YAG lasers at λ = 1064 nm and ∼10 μJ/pulse, the dynamics of tandem bubble interaction (individual maximum bubble diameter of 50 μm with a corresponding collapse time of 5.7 μs) are examined at different phase delays. In close proximity (i.e., interbubble distance = 40 μm or γ = 0.8), the tandem bubbles interact strongly with each other, leading to asymmetric deformation of the bubble walls and jet formation, as well as the production of two pairs of vortices in the surrounding fluid rotating in opposite directions. The direction and speed of the jet (up to 95 m/s), as well as the orientation and strength of the vortices can be varied by adjusting the phase delay.

Absorption and Metabolism of Phenolics from Digests of Polyphenol-Rich Potato Extracts Using the Caco-2/HepG2 Co-Culture System

PubMed Central

Sadeghi Ekbatan, Shima; Iskandar, Michele M.; Sleno, Lekha; Sabally, Kebba; Khairallah, Joelle; Prakash, Satya

2018-01-01

The bioactivity of dietary polyphenols depends upon gastrointestinal and hepatic metabolism of secondary microbial phenolic metabolites generated via colonic microbiota-mediated biotransformation. A polyphenol-rich potato extract (PRPE) containing chlorogenic, caffeic, and ferulic acids and rutin was digested in a dynamic multi-reactor gastrointestinal simulator of the human intestinal microbial ecosystem (GI model). Simulated digestion showed extensive degradation of the parent compounds and the generation of microbial phenolic metabolites. To characterize the transport and metabolism of microbial phenolic metabolites following digestion, a co-culture of intestinal Caco-2 and hepatic HepG2 cells was exposed to the PRPE-derived digests obtained from the colonic vessels. Following a 2 h incubation of the digesta with the Caco-2/HepG2 co-cultures, approximately 10–15% of ferulic, dihydrocaffeic, and dihydroferulic acids and 3–5% of 3-hydroxybenzoic, 3-hydroxyphenylpropionic, and coumaric acids were observed in the basolateral side, whereas 3-hydroxyphenylacetic acid, phenylpropanoic acid, and cinnamic acid were not detected. Subsequent HepG2 cellular metabolism led to major increases in ferulic, dihydrocaffeic, 3-hydroxyphenylpropionic, and coumaric acids ranging from 160–370%. These findings highlight the importance of hepatic metabolism towards the generation of secondary metabolites of polyphenols despite low selective Caco-2 cellular uptake of microbial phenolic metabolites. PMID:29329242

Electron-irradiated two-terminal, monolithic InP/Ga0.47In0.53As tandem solar cells and annealing of radiation damage

NASA Technical Reports Server (NTRS)

Cotal, H. L.; Walters, Robert J.; Summers, Geoffrey P.; Messenger, Scott R.

1994-01-01

Radiation damage results from two-terminal monolithic InP/Ga(0.47)In(0.53)As tandem solar cells subject to 1 MeV electron irradiation are presented. Efficiencies greater than 22 percent have been measured by the National Renewable Energy Laboratory from 2x2 sq cm cells at 1 sun, AMO (25 C). The short circuit current density, open circuit voltage and fill factor are found to tolerate the same amount of radiation at low fluences. At high fluence levels, slight differences are observed. Decreasing the base amount of radiation at the Ga(0.47)In(0.53)As bottomcell improved the radiation resistance of J(sub sc) dramatically. This is turn, extended the series current flow through the subcell substantially up to a fluence of 3x10(exp 15) cm(exp -2) compared to 3x10(exp 14) cm(exp -2), as observed previously. The degradation of the maximum power output form tandem device is comparable to that from shallow homojunction (SHJ) InP solar cells, and the mechanism responsible for such degradation is explained in terms of the radiation response of the component cells. Annealing studies revealed that the recovery of the tandem cell response is dictated by the annealing characteristics exhibited by SHJ InP solar cells.

On the Relativistic Correction of Particles Trajectory in Tandem Type Electrostatic Accelerator

NASA Astrophysics Data System (ADS)

Minárik, Stanislav

2015-08-01

A constant potential is applied to the acceleration of the ion-beam in the tandem type electrostatic accelerator. However, not just one voltage is applied, but instead a number of applications can be made in succession by means of the tandem arrangement of high voltage tubes. This number of voltage applications, which is the number of so-called "stages" of a tandem accelerator, may be two, three, or four, depending on the chosen design. Electrostatic field with approximately constant intensity acts on ions in any stage. In general, non-relativistic dynamics is used for the description of the ion transport in tandem accelerator. Energies of accelerated ions are too low and relativistic effects cannot be commonly observed by standard experimental technique. Estimation of possible relativistic correction of ion trajectories is therefore only a matter of calculation. In this note, we briefly present such calculation. Our aim is to show how using the relativistic dynamics modifies the particles trajectory in tandem type accelerator and what parameters determine this modification.

Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics.

PubMed

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information. Copyright © 2012 Wiley Periodicals, Inc.

Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions.

PubMed

Muramoto, Hiroki; Yagi, Shintaro; Hirabayashi, Keiji; Sato, Shinya; Ohgane, Jun; Tanaka, Satoshi; Shiota, Kunio

2010-08-01

Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome-wide DNA methylation modification status, as represented by the ESC-specific hypomethylation of tissue-dependent and differentially methylated regions (T-DMRs) of Pou5f1 and Nanog. Here, we conducted a genome-wide investigation of sequence characteristics associated with T-DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed elements (SINEs), long interspersed elements (LINEs) and long terminal repeats (LTRs). We found that hypomethylated T-DMRs were predominantly present in SINE-rich/LINE-poor genomic loci. The enrichment for SINEs spread over 300 kb in cis and there existed SINE-rich genomic domains spreading continuously over 1 Mb, which contained multiple hypomethylated T-DMRs. The characterization of sequence information showed that the enriched SINEs were relatively CpG rich and belonged to specific subfamilies. A subset of the enriched SINEs were hypomethylated T-DMRs in ESCs at Dppa3 gene locus, although SINEs are overall methylated in both ESCs and the liver. In conclusion, we propose that SINE enrichment is the genomic property of regions harboring hypomethylated T-DMRs in ESCs, which is a novel aspect of the ESC-specific epigenomic information.

Ultra-high performance liquid chromatography tandem mass spectrometry for the determination of five glycopeptide antibiotics in food and biological samples using solid-phase extraction.

PubMed

Deng, Fenfang; Yu, Hong; Pan, Xinhong; Hu, Guoyuan; Wang, Qiqin; Peng, Rongfei; Tan, Lei; Yang, Zhicong

2018-02-23

This paper demonstrated the development and validation of an ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for simultaneous determination of five glycopeptide antibiotics in food and biological samples. The target glycopeptide antibiotics were isolated from the samples by solvent extraction, and the extracts were cleaned with a tandem solid-phase extraction step using mixed strong cation exchange and hydrophilic/lipophilic balance cartridges. Subsequently, the analytes were eluted with different solvents, and then quantified by UHPLC-MS/MS in the positive ionization mode with multiple reaction monitoring. Under optimal conditions, good linear correlations were obtained for the five glycopeptide antibiotics in the concentration range of 1.0 μg/L to 20.0 μg/L, and with linear correlation coefficients >0.998. Employing this method, the target glycopeptide antibiotics in food and biological samples were identified with a recovery of 83.0-102%, and a low quantitation limit of 1.0 μg/kg in food and 2.0 μg/L in biological samples with low matrix effects. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of an advanced spacecraft tandem mass spectrometer

NASA Astrophysics Data System (ADS)

Drew, Russell C.

1992-03-01

The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

Development of an advanced spacecraft tandem mass spectrometer

NASA Technical Reports Server (NTRS)

Drew, Russell C.

1992-01-01

The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

PubMed

Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu

2013-01-04

Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .

Investigation of ASE and SRS effects on 1018nm short-wavelength Yb3+-doped fiber laser

NASA Astrophysics Data System (ADS)

Xie, Zhaoxin; Shi, Wei; Sheng, Quan; Fu, Shijie; Fang, Qiang; Zhang, Haiwei; Bai, Xiaolei; Shi, Guannan; Yao, Jianquan

2017-03-01

1018nm short wavelength Yb3+-doped fiber laser can be widely used for tandem-pumped fiber laser system in 1 μm regime because of its high brightness and low quantum defect (QD). In order to achieve 1018nm short wavelength Yb3+-doped fiber laser with high output power, a steady-state rate equations considering the amplified spontaneous emission (ASE) and Stimulated Raman Scattering (SRS) has been established. We theoretically analyzed the ASE and SRS effects in 1018nm short wavelength Yb3+-doped fiber laser and the simulation results show that the ASE is the main restriction rather than SRS for high power 1018nm short wavelength Yb3+-doped fiber laser, besides the high temperature of fiber is also the restriction for high output power. We use numerical solution of steady-state rate equations to discuss how to suppress ASE in 1018nm short wavelength fiber laser and how to achieve high power 1018nm short-wavelength fiber laser.

Ultra-Thin, Triple-Bandgap GaInP/GaAs/GaInAs Monolithic Tandem Solar Cells

NASA Technical Reports Server (NTRS)

Wanlass, M. W.; Ahrenkiel, S. P.; Albin, D. S.; Carapella, J. J.; Duda, A.; Emery, K.; Geisz, J. F.; Jones, K.; Kurtz, Sarah; Moriarty, T.;

All solution-processed lead halide perovskite-BiVO4 tandem assembly for photolytic solar fuels production.

PubMed

Chen, Yong-Siou; Manser, Joseph S; Kamat, Prashant V

2015-01-21

The quest for economic, large-scale hydrogen production has motivated the search for new materials and device designs capable of splitting water using only energy from the sun. Here we introduce an all solution-processed tandem water splitting assembly composed of a BiVO4 photoanode and a single-junction CH3NH3PbI3 hybrid perovskite solar cell. This unique configuration allows efficient solar photon management, with the metal oxide photoanode selectively harvesting high energy visible photons, and the underlying perovskite solar cell capturing lower energy visible-near IR wavelengths in a single-pass excitation. Operating without external bias under standard AM 1.5G illumination, the photoanode-photovoltaic architecture, in conjunction with an earth-abundant cobalt phosphate catalyst, exhibits a solar-to-hydrogen conversion efficiency of 2.5% at neutral pH. The design of low-cost tandem water splitting assemblies employing single-junction hybrid perovskite materials establishes a potentially promising new frontier for solar water splitting research.

Using hierarchical Bayesian multi-species mixture models to estimate tandem hoop-net based habitat associations and detection probabilities of fishes in reservoirs

USGS Publications Warehouse

Stewart, David R.; Long, James M.

2015-01-01

Species distribution models are useful tools to evaluate habitat relationships of fishes. We used hierarchical Bayesian multispecies mixture models to evaluate the relationships of both detection and abundance with habitat of reservoir fishes caught using tandem hoop nets. A total of 7,212 fish from 12 species were captured, and the majority of the catch was composed of Channel Catfish Ictalurus punctatus (46%), Bluegill Lepomis macrochirus(25%), and White Crappie Pomoxis annularis (14%). Detection estimates ranged from 8% to 69%, and modeling results suggested that fishes were primarily influenced by reservoir size and context, water clarity and temperature, and land-use types. Species were differentially abundant within and among habitat types, and some fishes were found to be more abundant in turbid, less impacted (e.g., by urbanization and agriculture) reservoirs with longer shoreline lengths; whereas, other species were found more often in clear, nutrient-rich impoundments that had generally shorter shoreline length and were surrounded by a higher percentage of agricultural land. Our results demonstrated that habitat and reservoir characteristics may differentially benefit species and assemblage structure. This study provides a useful framework for evaluating capture efficiency for not only hoop nets but other gear types used to sample fishes in reservoirs.

The origin and evolution of short-period Miras in the solar neighborhood: Constraints on the life cycle of old stars

NASA Technical Reports Server (NTRS)

Jura, M.

1994-01-01

The spatial distribution of the short-period (P less than 300 days) oxygen-rich Miras in the solar neighborhood can be fitted with an exponential scale height above the Galactic plane of about 600 pc. Using the Gliese catalog of local main-sequence stars, we estimate that the density of suitable G-type progenitor dwarfs within 20 pc of the Sun for these short-period Miras is 6 x 10(exp -4)/cu pc. The portion of the H-R diagram near the main-sequence turnoff of these velocity-selected Gliese stars is intermediate between that of the old open cluster NGC 188 and that of the metal-rich globular cluster, 47 Tuc. We infer that the main-sequence progenitors of the short-period Miras have masses near 1.0 solar mass, and we estimate that these Miras have ages approximately 9 x 10(exp 9). We also identify a few old disk red giants in the neighborhood of the Sun. On the basis of very limited information, we estimate that the total amount of mass lost from these stars during their first ascent up the red giant branch is less than or equal to 0.1 solar mass. We derive a duration of the short-period Mira phase of close to 5 x 10(exp 5) yr. This estimate for the duration of the short period Mira phase is longer than our estimate of 2 x 10(exp 5) yr for the duration of the Mira phase for stars with periods longer than 300 days. From their infrared colors, we estimate a typical mass-loss rate from the short-period Miras of approximately 1 x 10(exp -7) solar mass/yr.

Design and long-term monitoring of DSC/CIGS tandem solar module

NASA Astrophysics Data System (ADS)

Vildanova, M. F.; Nikolskaia, A. B.; Kozlov, S. S.; Shevaleevskiy, O. I.

2015-11-01

This paper describes the design and development of tandem dye-sensitized/Cu(In, Ga)Se (DSC/CIGS) PV modules. The tandem PV module comprised of the top DSC module and a bottom commercial 0,8 m2 CIGS module. The top DSC module was made of 10 DSC mini-modules with the field size of 20 × 20 cm2 each. Tandem DSC/CIGS PV modules were used for providing the long-term monitoring of energy yield and electrical parameters in comparison with standalone CIGS modules under outdoor conditions. The outdoor test facility, containing solar modules of both types and a measurement unit, was located on the roof of the Institute of Biochemical Physics in Moscow. The data obtained during monitoring within the 2014 year period has shown the advantages of the designed tandem DSC/CIGS PV-modules over the conventional CIGS modules, especially for cloudy weather and low-intensity irradiation conditions.

Determination of azithromycin residue in pork using a molecularly imprinted monolithic microcolumn coupled to liquid chromatography with tandem mass spectrometry.

PubMed

Zhou, Tong; Yang, Haicui; Jin, Zhen; Liu, Qingying; Song, Xuqin; He, Limin; Fang, Binghu; Meng, Chenying

2016-04-01

Using spiramycin as a dummy template, a molecularly imprinted polymer monolithic micro-column with high selection to azithromycin was prepared in a micropipette tip. The imprinting factor of the monolithic micro-column prepared was approximately 2.67 and the morphological structure of the polymers was characterized by scanning electron microscopy. A simple, sensitive, and reproducible method based on the imprinted monolithic micro-column coupled to liquid chromatography with tandem mass spectrometry was developed for determining the residues of azithromycin in pork. Pork samples were extracted with acetonitrile, cleaned up under the optimal monolithic micro-column conditions, and analyzed using liquid chromatography with tandem mass spectrometry in the multiple reaction monitoring mode. The assay exhibited a linear dynamic range of 0.50-50 μg/L with the correlation coefficient (r(2) ) above 0.99. In the three spiking levels of 0.50, 1.0, and 10 μg/kg, the average recoveries of azithromycin from pork samples were between 85.8 and 96.5% with a relative standard deviation below 10%. The limit of detection and limit of quantitation were 0.03 and 0.1 μg/kg, respectively. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Indirect Short- and Long-Term Effects of Aboveground Invertebrate and Vertebrate Herbivores on Soil Microarthropod Communities

PubMed Central

Vandegehuchte, Martijn L.; Raschein, Ursina; Schütz, Martin; Gwiazdowicz, Dariusz J.; Risch, Anita C.

2015-01-01

Recognition is growing that besides ungulates, small vertebrate and invertebrate herbivores are important drivers of grassland functioning. Even though soil microarthropods play key roles in several soil processes, effects of herbivores—especially those of smaller body size—on their communities are not well understood. Therefore, we progressively excluded large, medium and small vertebrate and invertebrate herbivores for three growing seasons using size-selective fences in two vegetation types in subalpine grasslands; short-grass and tall-grass vegetation generated by high and low historical levels of ungulate grazing. Herbivore exclusions generally had few effects on microarthropod communities, but exclusion of all herbivore groups resulted in decreased total springtail and Poduromorpha richness compared with exclusion of only ungulates and medium-sized mammals, regardless of vegetation type. The tall-grass vegetation had a higher total springtail richness and mesostigmatid mite abundance than the short-grass vegetation and a different oribatid mite community composition. Although several biotic and abiotic variables differed between the exclusion treatments and vegetation types, effects on soil microarthropods were best explained by differences in nutrient and fibre content of the previous year’s vegetation, a proxy for litter quality, and to a lesser extent soil temperature. After three growing seasons, smaller herbivores had a stronger impact on these functionally important soil microarthropod communities than large herbivores. Over longer time-scales, however, large grazers created two different vegetation types and thereby influenced microarthropod communities bottom-up, e.g. by altering resource quality. Hence, both short- and long-term consequences of herbivory affected the structure of the soil microarthropod community. PMID:25738942

Single P-N junction tandem photovoltaic device

DOEpatents

Walukiewicz, Wladyslaw [Kensington, CA; Ager, III, Joel W.; Yu, Kin Man [Lafayette, CA

2012-03-06

A single P-N junction solar cell is provided having two depletion regions for charge separation while allowing the electrons and holes to recombine such that the voltages associated with both depletion regions of the solar cell will add together. The single p-n junction solar cell includes an alloy of either InGaN or InAlN formed on one side of the P-N junction with Si formed on the other side in order to produce characteristics of a two junction (2J) tandem solar cell through only a single P-N junction. A single P-N junction solar cell having tandem solar cell characteristics will achieve power conversion efficiencies exceeding 30%.

Single P-N junction tandem photovoltaic device

DOEpatents

Walukiewicz, Wladyslaw [Kensington, CA; Ager, III, Joel W.; Yu, Kin Man [Lafayette, CA

2011-10-18

A single P-N junction solar cell is provided having two depletion regions for charge separation while allowing the electrons and holes to recombine such that the voltages associated with both depletion regions of the solar cell will add together. The single p-n junction solar cell includes an alloy of either InGaN or InAlN formed on one side of the P-N junction with Si formed on the other side in order to produce characteristics of a two junction (2J) tandem solar cell through only a single P-N junction. A single P-N junction solar cell having tandem solar cell characteristics will achieve power conversion efficiencies exceeding 30%.

Efficient Monolithic Perovskite/Silicon Tandem Solar Cell with Cell Area >1 cm(2).

PubMed

Werner, Jérémie; Weng, Ching-Hsun; Walter, Arnaud; Fesquet, Luc; Seif, Johannes Peter; De Wolf, Stefaan; Niesen, Bjoern; Ballif, Christophe

2016-01-07

Monolithic perovskite/crystalline silicon tandem solar cells hold great promise for further performance improvement of well-established silicon photovoltaics; however, monolithic tandem integration is challenging, evidenced by the modest performances and small-area devices reported so far. Here we present first a low-temperature process for semitransparent perovskite solar cells, yielding efficiencies of up to 14.5%. Then, we implement this process to fabricate monolithic perovskite/silicon heterojunction tandem solar cells yielding efficiencies of up to 21.2 and 19.2% for cell areas of 0.17 and 1.22 cm(2), respectively. Both efficiencies are well above those of the involved subcells. These single-junction perovskite and tandem solar cells are hysteresis-free and demonstrate steady performance under maximum power point tracking for several minutes. Finally, we present the effects of varying the intermediate recombination layer and hole transport layer thicknesses on tandem cell photocurrent generation, experimentally and by transfer matrix simulations.

Methane Emission and Milk Production of Dairy Cows Grazing Pastures Rich in Legumes or Rich in Grasses in Uruguay

PubMed Central

Dini, Yoana; Gere, José; Briano, Carolina; Manetti, Martin; Juliarena, Paula; Picasso, Valentin; Gratton, Roberto; Astigarraga, Laura

2012-01-01

Simple Summary GHGs emissions are relevant in evaluating environmental impact of farming systems. Methane (CH4) produced by enteric fermentation accounts for half of all anthropogenic emissions of GHGs in Uruguay, where ruminant production is based on year round grazing of forages. Here we compared milk production and CH4 emissions by dairy cows grazing two contrasting mixed pastures (rich in legumes or rich in grasses) using the SF6 tracer technique adapted to collect breath samples over 5-days periods. There were no differences in milk or CH4 production between the contrasting pastures, probably because of the high herbage allowance that enabled selective grazing by cows. Abstract Understanding the impact of changing pasture composition on reducing emissions of GHGs in dairy grazing systems is an important issue to mitigate climate change. The aim of this study was to estimate daily CH4 emissions of dairy cows grazing two mixed pastures with contrasting composition of grasses and legumes: L pasture with 60% legumes on Dry Matter (DM) basis and G pasture with 75% grasses on DM basis. Milk production and CH4 emissions were compared over two periods of two weeks during spring using eight lactating Holstein cows in a 2 × 2 Latin square design. Herbage organic matter intake (HOMI) was estimated by chromic oxide dilution and herbage organic matter digestibility (OMD) was estimated by faecal index. Methane emission was estimated by using the sulfur hexafluoride (SF6) tracer technique adapted to collect breath samples over 5-day periods. OMD (0.71) and HOMI (15.7 kg OM) were not affected by pasture composition. Milk production (20.3 kg/d), milk fat yield (742 g/d) and milk protein yield (667 g/d) were similar for both pastures. This may be explained by the high herbage allowance (30 kg DM above 5 cm/cow) which allowed the cows to graze selectively, in particular in grass sward. Similarly, methane emission expressed as absolute value (368 g/d or 516 L/d) or expressed as

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

PubMed

Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

2016-03-01

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

Additional testing of the inlets designed for a tandem fan V/STOL nacelle

NASA Technical Reports Server (NTRS)

Ybarra, A. H.

1981-01-01

The wind tunnel testing of a scale model of a tandem fan nacelle designed for a type (subsonic cruise) V/STOL aircraft configuration is discussed. The performance for the isolated front inlet and for the combined front and aft inlets is reported. Model variables include front and aft inlets with aft inlet variations of short and long aft inlet cowls, with a shaft simulator and diffuser vortex generators, cowl lip fillets, and nacelle strakes. Inlet pressure recovery, distortion, and inlet angle-to-attack separation limits were evaluated at tunnel velocity from 0 to 240 knots, angles-of-attack from -10 to +40 degrees and inlet flow rates corresponding to throat Mach number from 0.0 to 0.6. Combined nacelle pitch and yaw runs up to 30 deg. were also made.

Haptic information provided by the "anchor system" reduces trunk sway acceleration in the frontal plane during tandem walking in older adults.

PubMed

Costa, Andréia Abud da Silva; Manciopi, Priscila Abbári Rossi; Mauerberg-deCastro, Eliane; Moraes, Renato

2015-11-16

This study assessed whether the use of an "anchor system" benefited older adults who performed a tandem walking task. Additionally, we tested the effects of practice with the anchor system during walking on trunk stability, in the frontal plane, of older adults. Forty-four older adults were randomly assigned to three groups: control group, 0g anchor group, and 125g anchor group. Individuals in each group performed a tandem walking task on the GaitRite system with an accelerometer placed on the cervical region. The participants in the 125g anchor group held, in each hand, a flexible cable with a light mass attached at the end of the cable, which rested on the ground. While the participants walked, they pulled on the cables just enough to keep them taut as the masses slid over the ground. The 0g anchor group held an anchor tool without any mass attached to the end portion. The results of this study demonstrated that the use of the anchor system contributed to the reduction of trunk acceleration in the frontal plane. However, this effect did not persist after removal of the anchors, which suggests that the amount of practice with this tool was insufficient to generate any lasting effect, or that the task was not sufficiently challenging, or both. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system.

PubMed

Yosef, Ido; Goren, Moran G; Kiro, Ruth; Edgar, Rotem; Qimron, Udi

2011-12-13

Prokaryotic DNA arrays arranged as clustered regularly interspaced short palindromic repeats (CRISPR), along with their associated proteins, provide prokaryotes with adaptive immunity by RNA-mediated targeting of alien DNA or RNA matching the sequences between the repeats. Here, we present a thorough screening system for the identification of bacterial proteins participating in immunity conferred by the Escherichia coli CRISPR system. We describe the identification of one such protein, high-temperature protein G (HtpG), a homolog of the eukaryotic chaperone heat-shock protein 90. We demonstrate that in the absence of htpG, the E. coli CRISPR system loses its suicidal activity against λ prophage and its ability to provide immunity from lysogenization. Transcomplementation of htpG restores CRISPR activity. We further show that inactivity of the CRISPR system attributable to htpG deficiency can be suppressed by expression of Cas3, a protein that is essential for its activity. Accordingly, we also find that the steady-state level of overexpressed Cas3 is significantly enhanced following HtpG expression. We conclude that HtpG is a newly identified positive modulator of the CRISPR system that is essential for maintaining functional levels of Cas3.

High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system

PubMed Central

Yosef, Ido; Goren, Moran G.; Kiro, Ruth; Edgar, Rotem; Qimron, Udi

2011-01-01

Prokaryotic DNA arrays arranged as clustered regularly interspaced short palindromic repeats (CRISPR), along with their associated proteins, provide prokaryotes with adaptive immunity by RNA-mediated targeting of alien DNA or RNA matching the sequences between the repeats. Here, we present a thorough screening system for the identification of bacterial proteins participating in immunity conferred by the Escherichia coli CRISPR system. We describe the identification of one such protein, high-temperature protein G (HtpG), a homolog of the eukaryotic chaperone heat-shock protein 90. We demonstrate that in the absence of htpG, the E. coli CRISPR system loses its suicidal activity against λ prophage and its ability to provide immunity from lysogenization. Transcomplementation of htpG restores CRISPR activity. We further show that inactivity of the CRISPR system attributable to htpG deficiency can be suppressed by expression of Cas3, a protein that is essential for its activity. Accordingly, we also find that the steady-state level of overexpressed Cas3 is significantly enhanced following HtpG expression. We conclude that HtpG is a newly identified positive modulator of the CRISPR system that is essential for maintaining functional levels of Cas3. PMID:22114197

Hybrid tandem quantum dot/organic photovoltaic cells with complementary near infrared absorption

NASA Astrophysics Data System (ADS)

Kim, Taesoo; Palmiano, Elenita; Liang, Ru-Ze; Hu, Hanlin; Murali, Banavoth; Kirmani, Ahmad R.; Firdaus, Yuliar; Gao, Yangqin; Sheikh, Arif; Yuan, Mingjian; Mohammed, Omar F.; Hoogland, Sjoerd; Beaujuge, Pierre M.; Sargent, Edward H.; Amassian, Aram

2017-05-01

Monolithically integrated hybrid tandem solar cells that effectively combine solution-processed colloidal quantum dot (CQD) and organic bulk heterojunction subcells to achieve tandem performance that surpasses the individual subcell efficiencies have not been demonstrated to date. In this work, we demonstrate hybrid tandem cells with a low bandgap PbS CQD subcell harvesting the visible and near-infrared photons and a polymer:fullerene—poly (diketopyrrolopyrrole-terthiophene) (PDPP3T):[6,6]-phenyl-C60-butyric acid methyl ester (PC61BM)—top cell absorbing effectively the red and near-infrared photons of the solar spectrum in a complementary fashion. The two subcells are connected in series via an interconnecting layer (ICL) composed of a metal oxide layer, a conjugated polyelectrolyte, and an ultrathin layer of Au. The ultrathin layer of Au forms nano-islands in the ICL, reducing the series resistance, increasing the shunt resistance, and enhancing the device fill-factor. The hybrid tandems reach a power conversion efficiency (PCE) of 7.9%, significantly higher than the PCE of the corresponding individual single cells, representing one of the highest efficiencies reported to date for hybrid tandem solar cells based on CQD and polymer subcells.

Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum (cv. Heinz 1706).

PubMed

Krsticevic, Flavia J; Arce, Débora P; Ezpeleta, Joaquín; Tapia, Elizabeth

2016-10-13

In plants, fruit maturation and oxidative stress can induce small heat shock protein (sHSP) synthesis to maintain cellular homeostasis. Although the tomato reference genome was published in 2012, the actual number and functionality of sHSP genes remain unknown. Using a transcriptomic (RNA-seq) and evolutionary genomic approach, putative sHSP genes in the Solanum lycopersicum (cv. Heinz 1706) genome were investigated. A sHSP gene family of 33 members was established. Remarkably, roughly half of the members of this family can be explained by nine independent tandem duplication events that determined, evolutionarily, their functional fates. Within a mitochondrial class subfamily, only one duplicated member, Solyc08g078700, retained its ancestral chaperone function, while the others, Solyc08g078710 and Solyc08g078720, likely degenerated under neutrality and lack ancestral chaperone function. Functional conservation occurred within a cytosolic class I subfamily, whose four members, Solyc06g076570, Solyc06g076560, Solyc06g076540, and Solyc06g076520, support ∼57% of the total sHSP RNAm in the red ripe fruit. Subfunctionalization occurred within a new subfamily, whose two members, Solyc04g082720 and Solyc04g082740, show heterogeneous differential expression profiles during fruit ripening. These findings, involving the birth/death of some genes or the preferential/plastic expression of some others during fruit ripening, highlight the importance of tandem duplication events in the expansion of the sHSP gene family in the tomato genome. Despite its evolutionary diversity, the sHSP gene family in the tomato genome seems to be endowed with a core set of four homeostasis genes: Solyc05g014280, Solyc03g082420, Solyc11g020330, and Solyc06g076560, which appear to provide a baseline protection during both fruit ripening and heat shock stress in different tomato tissues. Copyright © 2016 Krsticevic et al.

Optical enhancement of a printed organic tandem solar cell using diffractive nanostructures.

PubMed

Mayer, Jan A; Offermans, Ton; Chrapa, Marek; Pfannmöller, Martin; Bals, Sara; Ferrini, Rolando; Nisato, Giovanni

2018-03-19

Solution processable organic tandem solar cells offer a promising approach to achieve cost-effective, lightweight and flexible photovoltaics. In order to further enhance the efficiency of optimized organic tandem cells, diffractive light-management nanostructures were designed for an optimal redistribution of the light as function of both wavelength and propagation angles in both sub-cells. As the fabrication of these optical structures is compatible with roll-to-roll production techniques such as hot-embossing or UV NIL imprinting, they present an optimal cost-effective solution for printed photovoltaics. Tandem cells with power conversion efficiencies of 8-10% were fabricated in the ambient atmosphere by doctor blade coating, selected to approximate the conditions during roll-to-roll manufacturing. Application of the light management structure onto an 8.7% efficient encapsulated tandem cell boosted the conversion efficiency of the cell to 9.5%.

pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

PubMed

Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

2009-11-23

Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

Modified tandem gratings anastigmatic imaging spectrometer with oblique incidence for spectral broadband

NASA Astrophysics Data System (ADS)

Cui, Chengguang; Wang, Shurong; Huang, Yu; Xue, Qingsheng; Li, Bo; Yu, Lei

2015-09-01

A modified spectrometer with tandem gratings that exhibits high spectral resolution and imaging quality for solar observation, monitoring, and understanding of coastal ocean processes is presented in this study. Spectral broadband anastigmatic imaging condition, spectral resolution, and initial optical structure are obtained based on geometric aberration theory. Compared with conventional tandem gratings spectrometers, this modified design permits flexibility in selecting gratings. A detailed discussion of the optical design and optical performance of an ultraviolet spectrometer with tandem gratings is also included to explain the advantage of oblique incidence for spectral broadband.

Tandem photovoltaic solar cells and increased solar energy conversion efficiency

NASA Technical Reports Server (NTRS)

Loferski, J. J.

1976-01-01

Tandem photovoltaic cells, as proposed by Jackson (1955) to increase the efficiency of solar energy conversion, involve the construction of a system of stacked p/n homojunction photovoltaic cells composed of different semiconductors. It had been pointed out by critics, however, that the total power which could be extracted from the cells in the stack placed side by side was substantially greater than the power obtained from the stacked cells. A reexamination of the tandem cell concept in view of the development of the past few years is conducted. It is concluded that the use of tandem cell systems in flat plate collectors, as originally envisioned by Jackson, may yet become feasible as a result of the development of economically acceptable solar cells for large scale terrestrial power generation.

Food plant diversity as broad-scale determinant of avian frugivore richness

PubMed Central

Kissling, W. Daniel; Rahbek, Carsten; Böhning-Gaese, Katrin

2007-01-01

The causes of variation in animal species richness at large spatial scales are intensively debated. Here, we examine whether the diversity of food plants, contemporary climate and energy, or habitat heterogeneity determine species richness patterns of avian frugivores across sub-Saharan Africa. Path models indicate that species richness of Ficus (their fruits being one of the major food resources for frugivores in the tropics) has the strongest direct effect on richness of avian frugivores, whereas the influences of variables related to water–energy and habitat heterogeneity are mainly indirect. The importance of Ficus richness for richness of avian frugivores diminishes with decreasing specialization of birds on fruit eating, but is retained when accounting for spatial autocorrelation. We suggest that a positive relationship between food plant and frugivore species richness could result from niche assembly mechanisms (e.g. coevolutionary adaptations to fruit size, fruit colour or vertical stratification of fruit presentation) or, alternatively, from stochastic speciation–extinction processes. In any case, the close relationship between species richness of Ficus and avian frugivores suggests that figs are keystone resources for animal consumers, even at continental scales. PMID:17251107

Fission and Properties of Neutron-Rich Nuclei

NASA Astrophysics Data System (ADS)

Hamilton, Joseph H.; Ramayya, A. V.; Carter, H. K.

2008-08-01

Opening session. Nuclear processes in stellar explosions / M. Wiescher. In-beam [symbol]-ray spectroscopy of neutron-rich nuclei at NSCL / A. Gade -- Nuclear structure I. Shell-model structure of neutron-rich nuclei beyond [symbol]Sn / A. Covello ... [et al.]. Shell structure and evolution of collectivity in nuclei above the [symbol]Sn core / S. Sarkar and M. S. Sarkar. Heavy-ion fusion using density-constrained TDHF / A. S. Umar and V. E. Oberacker. Towards an extended microscopic theory for upper-fp shell nuclei / K. P. Drumev. Properties of the Zr and Pb isotopes near the drip-line / V. N. Tarasov ... [et al.]. Identification of high spin states in [symbol] Cs nuclei and shell model calculations / K. Li ... [et al.]. Recent measurements of spherical and deformed isomers using the Lohengrin fission-fragment spectrometer / G. S. Simpson ... [et al.] -- Nuclear structure II. Nuclear structure investigation with rare isotope spectroscopic investigations at GSI / P. Boutachkov. Exploring the evolution of the shell structures by means of deep inelastic reactions / G. de Anaelis. Probing shell closures in neutron-rich nuclei / R. Krücken for the S277 and REX-ISOLDEMINIBALL collaborations. Structure of Fe isotopes at the limits of the pf-shell / N. Hoteling ... [et al.]. Spectroscopy of K isomers in shell-stabilized trans-fermium nuclei / S. K. Tandel ... [et al.] -- Radioactive ion beam facilities. SPIRAL2 at GANIL: a world leading ISOL facility for the next decade / S. Gales. New physics at the International Facility for Antiproton and Ion Research (FAIR) next to GSI / I. Augustin ... [et al.]. Radioactive beams from a high powered ISOL system / A. C. Shotter. RlKEN RT beam factory / T. Motobayashi. NSCL - ongoing activities and future perspectives / C. K. Gelbke. Rare isotope beams at Argonne / W. F. Henning. HRIBF: scientific highlights and future prospects / J. R. Beene. Radioactive ion beam research done in Dubna / G. M. Ter-Akopian ... [et al.] -- Fission I

Abundances in metal-rich stars. Detailed abundance analysis of 47 G and K dwarf stars with [Me/H] > 0.10 dex

NASA Astrophysics Data System (ADS)

Feltzing, S.; Gustafsson, B.

1998-04-01

We have derived elemental abundances of O, Na, Mg, Al, Si, Ca, Ti, Cr, Mn, Fe, Co, Ni as well as for a number of s-elements for 47 G and K dwarf, with [Me/H]>0.1 dex. The selection of stars was based on their kinematics as well as on their uvby-beta photometry. One sample of stars on rather eccentric orbits traces the chemical evolution interior to the solar orbit and another, on circular orbits, the evolution around the solar orbit. A few Extreme Population I stars were included in the latter sample. The stars have -0.1 dex < [Fe/H] < 0.42 dex. The spectroscopic [Fe/H] correlate well with the [Me/H] derived from uvby-beta photometry. We find that the elemental abundances of Mg, Al, Si, Ca, Ti, Cr and Ni all follow [Fe/H]. Our data put further constraints on models of galactic chemical evolution, in particular of Cr, Mn and Co which have not previously been studied for dwarf stars with [Me/H] >0.1 dex. The increase in [Na/Fe] and [Al/Fe] as a function of [Fe/H] found previously by \\cite[Edvardsson et al. (1993a)]{Edv93} has been confirmed for [Na/Fe]. This upturning relation, and the scatter around it, are shown not to be due to a mixture of populations with different mean distances to the galactic centre. We do not confirm the same trend for aluminium, which is somewhat surprising since both these elements are thought to be produced in the same environments in the pre-supernova stars. Nor have we been able to trace any tendency for relative abundances of O, Si, and Ti relative to Fe to vary with the stellar velocities, i.e. the stars present mean distance to the galactic centre. These results imply that there is no significant difference in the chemical evolution of the different stellar populations for stars with [Me/H]>0.1 dex. We find that [O/Fe] continue to decline with increasing [Fe/H] and that oxygen and europium correlate well. However [Si/Fe] and [Ca/Fe] seem to stay constant. A real (``cosmic'') scatter in [Ti/Fe] at given [Fe/H] is suggested as well as

Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

PubMed

Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

2016-09-01

The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

PubMed Central

2010-01-01

Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands. PMID:20500903

Sown species richness and realized diversity can influence functioning of plant communities differently.

PubMed

Rychtecká, Terezie; Lanta, Vojtěch; Weiterová, Iva; Lepš, Jan

2014-08-01

Biodiversity-ecosystem functioning experiments (BEF) typically manipulate sown species richness and composition of experimental communities to study ecosystem functioning as a response to changes in diversity. If sown species richness is taken as a measure of diversity and aboveground biomass production as a measure of community functioning, then this relationship is usually found to be positive. The sown species richness can be considered the equivalent of a local species pool in natural communities. However, in addition to species richness, realized diversity is also an important community diversity component. Realized diversity is affected by environmental filtering and biotic interactions operating within a community. As both sown species richness and the realized diversity in BEF studies (as well as local species pool vs observed realized richness in natural communities) can differ markedly, so can their effects on the community functioning. We tested this assumption using two data sets: data from a short-term pot experiment and data from the long-term Jena biodiversity plot experiment. We considered three possible predictors of community functioning (aboveground biomass production): sown species richness, realized diversity (defined as inverse of Simpson dominance index), and survivor species richness. Sown species richness affected biomass production positively in all cases. Realized diversity as well as survivor species richness had positive effects on biomass in approximately half of cases. When realized diversity or survivor species richness was tested together with sown species richness, their partial effects were none or negative. Our results suggest that we can expect positive diversity-productivity relationship when the local species pool size is the decisive factor determining realized observed diversity; in other cases, the shape of the diversity-functioning relationship may be quite opposite.

Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure.

PubMed

Borodulina, O R; Kramerov, D A

2001-10-01

Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.

One step derivatization with British Anti-Lewsite in combination with gas chromatography coupled to triple-quadrupole tandem mass spectrometry for the fast and selective analysis of inorganic arsenic in rice.

PubMed

Kang, Ju Hui; Jung, Hyun Jeong; Jung, Mun Yhung

2016-08-31

We developed a new fast and selective analytical method for the determination of inorganic arsenic (iAs) in rice by a gas chromatography - tandem mass spectrometry (GC-MS/MS) in combination with one step derivatization of inorganic arsenic (iAs) with British Anti-Lewsite (BAL). Two step derivatization of iAs with BAL has been previously performed for the GC-MS analysis. In this paper, the quantitative one step derivatization condition was successfully established. The GC-MS/MS was carried out with a short nonpolar capillary column (0.25 mm × 10 m) under the conditions of fast oven temperature ramp rate (4 °C/s) and high linear velocity (108.8 cm/s) of the carrier gas. The established GC-MS/MS method showed an excellent linearity (r(2) > 0.999) in a tested range (0.2-100.0 μg L(-1)), ultra-low limit of detection (LOD, 0.08 pg), and high precision and accuracy. The GC-MS/MS technique showed far greater selectivity (22.5 fold higher signal to noise ratio in rice sample) on iAs than GC-MS method. The gas chromatographic running time was only 2.5 min with the iAs retention time of 1.98 min. The established method was successfully applied to quantify the iAs contents in polished rice. The mean iAs content in the Korean polished rice (n = 27) was 66.1 μg kg(-1) with the range of 37.5-125.0 μg kg(-1). This represents the first report on the GC-tandem mass spectrometry in combination with the one step derivatization with BAL for the iAs speciation in rice. This GC-MS/MS method would be a simple, useful and reliable measure for the iAs analysis in rice in the laboratories in which the expensive and element specific HPLC-ICP-MS is not available. Copyright © 2016 Elsevier B.V. All rights reserved.

Microstructures and formation history of melilite-rich calcium-aluminum-rich inclusions from the ALHA77307 CO3.0 chondrite

NASA Astrophysics Data System (ADS)

Han, Jangmi; Brearley, Adrian J.

2017-03-01

We have studied four melilite-rich calcium-aluminum-rich inclusions (CAIs) from the Allan Hills A77307 CO3.0 chondrite using transmission electron microscopy with the focused ion beam sample preparation technique. This type of CAI represents one of the dominant types of refractory inclusions in CO3 chondrites. Individual melilite-rich CAIs 04-07 record complex formational histories involving high-temperature gas-solid condensation that occurred under both equilibrium and disequilibrium conditions. CAI 04 contains two texturally- and compositionally-distinct occurrences of perovskite: fine-grained perovskite within a melilite-rich core and aggregates of perovskite grains that surround the core. The perovskite in the core was probably involved in a disequilibrium reaction with early equilibrium condensates (e.g., melilite and spinel) and a nebular gas to form Al-Ti-rich diopside, followed by a later condensation of the perovskite aggregates under equilibrium conditions. CAI 05 has a compact melilite-rich core surrounded by a porous mantle, and likely formed by at least two different condensation events under equilibrium and disequilibrium conditions. In CAI 06, complex intergrowth layers of spinel and diopside surrounding a melilite-rich core indicate disequilibrium reaction of spinel and melilite with a nebular gas to form Al-Ti-rich diopside following core formation by equilibrium condensation. CAI 07 is dominated by melilite with a narrow compositional range and equilibrated textures, suggesting its formation by equilibrium condensation over a limited temperature range. Collectively, we infer that the melilite-rich inclusions formed by a generalized sequence of high-temperature gas-solid condensation that involved: (1) formation of CAI cores by aggregation of primary equilibrium condensates (i.e., perovskite, spinel, and melilite), (2) back-reactions of the primary core minerals with a nebular gas under disequilibrium conditions, forming diopside that evolves in

Numerical investigation & comparison of a tandem-bladed turbocharger centrifugal compressor stage with conventional design

NASA Astrophysics Data System (ADS)

Danish, Syed Noman; Qureshi, Shafiq Rehman; EL-Leathy, Abdelrahman; Khan, Salah Ud-Din; Umer, Usama; Ma, Chaochen

2014-12-01

Extensive numerical investigations of the performance and flow structure in an unshrouded tandem-bladed centrifugal compressor are presented in comparison to a conventional compressor. Stage characteristics are explored for various tip clearance levels, axial spacings and circumferential clockings. Conventional impeller was modified to tandem-bladed design with no modifications in backsweep angle, meridional gas passage and camber distributions in order to have a true comparison with conventional design. Performance degradation is observed for both the conventional and tandem designs with increase in tip clearance. Linear-equation models for correlating stage characteristics with tip clearance are proposed. Comparing two designs, it is clearly evident that the conventional design shows better performance at moderate flow rates. However; near choke flow, tandem design gives better results primarily because of the increase in throat area. Surge point flow rate also seems to drop for tandem compressor resulting in increased range of operation.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

PubMed

Melters, Daniël P; Bradnam, Keith R; Young, Hugh A; Telis, Natalie; May, Michael R; Ruby, J Graham; Sebra, Robert; Peluso, Paul; Eid, John; Rank, David; Garcia, José Fernando; DeRisi, Joseph L; Smith, Timothy; Tobias, Christian; Ross-Ibarra, Jeffrey; Korf, Ian; Chan, Simon W L

2013-01-30

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

PubMed Central

2013-01-01

Background Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Results Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. Conclusions While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. PMID:23363705

Peptide Identification by Database Search of Mixture Tandem Mass Spectra*

PubMed Central

Wang, Jian; Bourne, Philip E.; Bandeira, Nuno

2011-01-01

In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision. PMID:21862760

Tandem truncated rotavirus VP8* subunit protein with T cell epitope as non-replicating parenteral vaccine is highly immunogenic.

PubMed

Wen, Xiaobo; Cao, Dianjun; Jones, Ronald W; Hoshino, Yasutaka; Yuan, Lijuan

2015-01-01

The two currently available live oral rotavirus vaccines, Rotarix(®) and RotaTeq(®), are highly efficacious in the developed countries. However, the efficacy of such vaccines in resource deprived countries in Africa and Southeast Asia is low. We reported previously that a bacterially-expressed rotavirus P2-P[8] ΔVP8* subunit vaccine candidate administered intramuscularly elicited high-titers of neutralizing antibodies in guinea pigs and mice and significantly shortened the duration of diarrhea in neonatal gnotobiotic pigs upon oral challenge with virulent human rotavirus Wa strain. To further improve its vaccine potential and provide wider coverage against rotavirus strains of global and regional epidemiologic importance, we constructed 2 tandem recombinant VP8* proteins, P2-P[8] ΔVP8*-P[8] ΔVP8* and P2-P[8] ΔVP8*-P[6] ΔVP8* based on Escherichia coli expression system. The two resulting recombinant tandem proteins were highly soluble and P2-P[8] ΔVP8*-P[8] ΔVP8* was generated with high yield. Moreover, guinea pigs immunized intramuscularly by 3 doses of the P2-P[8] ΔVP8*-P[8] ΔVP8* or P2-P[8] ΔVP8*-P[6] ΔVP8* vaccine with aluminum phosphate adjuvant developed high titers of homotypic and heterotypic neutralizing antibodies against human rotaviruses bearing G1-G4, G8, G9 and G12 with P[8], P[4] or P[6] combination. The results suggest that these 2 subunit vaccines in monovalent or bivalent formulation can provide antigenic coverage to almost all the rotavirus G (VP7) types and major P (VP4) types of global as well as regional epidemiologic importance.

Haemolytic and Antimicrobial Activites of Saponin-Rich Extracts from Guar Meal

USDA-ARS?s Scientific Manuscript database

Saponin-rich GM extract was prepared by refluxing 25 g of GM with 250 ml of EtOH/H2O (1:1, v/v) for 3 h then filtering and distilling EtOH at 50oC. The refluxed extract was partitioned with equal volume of BuOH obtaining crude saponin-rich GM extract with 4.8 ± 0.6% DM of GM that was purified by RP...

[Liquid chromatography-tandem mass spectrometry method for determination of 10 macrolide antibiotics in pork samples using on-line solid phase extraction purification].

PubMed

Zhang, Xiaoguang; Liu, Dong; Liu, Hongran; Li, Qiang; Li, Lili; Wang, Lixia; Zhang, Yan

2017-10-08

A high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method based on-line solid phase extraction (SPE) purification was established to determine 10 macrolide antibiotics in pork samples. The samples were extracted with acetonitrile, and the extracts were dried with rotary evaporator at 40℃, then the analytes were dissolved with 2 mL phosphate buffer. The solutions were purified and concentrated by on-line SPE with HLB cartridges. The analytes were eluted with methanol, and then transferred to XBridge BEH C18 column, separated with the mobile phases of 10 mmol/L ammonium acetate aqueous solution and acetonitrile. Finally, the target analytes were detected by tandem mass spectrometry. The results showed that good linearity was obtained in the range of 0.1-200 μg/L for the 10 macrolide antibiotics with correlation coefficients better than 0.990. The limits of detection were in range of 0.05-0.30 μg/kg and the limits of quantitation were in range of 0.10-1.00 μg/kg. The recoveries of the method were in range of 69.6%-115.2% at the spiked levels of 0.10-10.0 μg/kg for all analytes, with the relative standard deviations less than 10%. The developed method can be used for the determination of the 10 macrolide antibiotics in pork samples.

Diversification rates and species richness across the Tree of Life

PubMed Central

Scholl, Joshua P.

2016-01-01

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. PMID:27605507

Tunable color parallel tandem organic light emitting devices with carbon nanotube and metallic sheet interlayers

NASA Astrophysics Data System (ADS)

Oliva, Jorge; Papadimitratos, Alexios; Desirena, Haggeo; De la Rosa, Elder; Zakhidov, Anvar A.

2015-11-01

Parallel tandem organic light emitting devices (OLEDs) were fabricated with transparent multiwall carbon nanotube sheets (MWCNT) and thin metal films (Al, Ag) as interlayers. In parallel monolithic tandem architecture, the MWCNT (or metallic films) interlayers are an active electrode which injects similar charges into subunits. In the case of parallel tandems with common anode (C.A.) of this study, holes are injected into top and bottom subunits from the common interlayer electrode; whereas in the configuration of common cathode (C.C.), electrons are injected into the top and bottom subunits. Both subunits of the tandem can thus be monolithically connected functionally in an active structure in which each subunit can be electrically addressed separately. Our tandem OLEDs have a polymer as emitter in the bottom subunit and a small molecule emitter in the top subunit. We also compared the performance of the parallel tandem with that of in series and the additional advantages of the parallel architecture over the in-series were: tunable chromaticity, lower voltage operation, and higher brightness. Finally, we demonstrate that processing of the MWCNT sheets as a common anode in parallel tandems is an easy and low cost process, since their integration as electrodes in OLEDs is achieved by simple dry lamination process.

Tandem betatron

DOEpatents

Keinigs, Rhonald K.

1992-01-01

Two betatrons are provided in tandem for alternately accelerating an electron beam to avoid the single flux swing limitation of conventional betatrons and to accelerate the electron beam to high energies. The electron beam is accelerated in a first betatron during a period of increasing magnetic flux. The eletron beam is extracted from the first betatron as a peak magnetic flux is reached and then injected into a second betatron at a time of minimum magnetic flux in the second betatron. The cycle may be repeated until the desired electron beam energy is obtained. In one embodiment, the second betatron is axially offset from the first betatron to provide for electron beam injection directly at the axial location of the beam orbit in the second betatron.

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass.

PubMed

Hiiesalu, Inga; Pärtel, Meelis; Davison, John; Gerhold, Pille; Metsis, Madis; Moora, Mari; Öpik, Maarja; Vasar, Martti; Zobel, Martin; Wilson, Scott D

2014-07-01

Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above- and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root-colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454-sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below- than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Effects of short-chain chlorinated paraffins exposure on the viability and metabolism of human hepatoma HepG2 cells.

PubMed

Geng, Ningbo; Zhang, Haijun; Zhang, Baoqin; Wu, Ping; Wang, Feidi; Yu, Zhengkun; Chen, Jiping

2015-03-03

Short-chain chlorinated paraffins (SCCPs) have attracted considerable attention for their characteristic of persistent organic pollutants. However, very limited information is available for their toxic effects at environmentally relevant doses, limiting the evaluation of their health risks. In this study, cell viability assay and targeted metabolomic approach was used to evaluate the environmental dose (<100 μg/L) effect of SCCPs on HepG2 cells. Cell viability was found to be decreased with increases in exposure dose of SCCPs. Exposure for 48 h to C10-CPs resulted in a significant reduction in cell viability compared with 24 h, even at 1 μg/L. SCCPs exposure altered the intracellular redox status and caused significant metabolic disruptions. As a kind of peroxisome proliferator, SCCPs specifically stimulated the β-oxidation of unsaturated fatty acids and long-chain fatty acids. Meanwhile, SCCPs exposure disturbed glycolysis and amino acid metabolism, and led to the up-regulation of glutamate metabolism and urea cycle. The toxic effects of SCCPs might mainly involve the perturbation of energy production, protein biosynthesis, fatty acid metabolism, and ammonia recycling.

Leucine-rich repeat-containing G protein-coupled receptor 4 facilitates vesicular stomatitis virus infection by binding vesicular stomatitis virus glycoprotein.

PubMed

Zhang, Na; Huang, Hongjun; Tan, Binghe; Wei, Yinglei; Xiong, Qingqing; Yan, Yan; Hou, Lili; Wu, Nannan; Siwko, Stefan; Cimarelli, Andrea; Xu, Jianrong; Han, Honghui; Qian, Min; Liu, Mingyao; Du, Bing

2017-10-06

Vesicular stomatitis virus (VSV) and rabies and Chandipura viruses belong to the Rhabdovirus family. VSV is a common laboratory virus to study viral evolution and host immune responses to viral infection, and recombinant VSV-based vectors have been widely used for viral oncolysis, vaccination, and gene therapy. Although the tropism of VSV is broad, and its envelope glycoprotein G is often used for pseudotyping other viruses, the host cellular components involved in VSV infection remain unclear. Here, we demonstrate that the host protein leucine-rich repeat-containing G protein-coupled receptor 4 (Lgr4) is essential for VSV and VSV-G pseudotyped lentivirus (VSVG-LV) to infect susceptible cells. Accordingly, Lgr4-deficient mice had dramatically decreased VSV levels in the olfactory bulb. Furthermore, Lgr4 knockdown in RAW 264.7 cells also significantly suppressed VSV infection, and Lgr4 overexpression in RAW 264.7 cells enhanced VSV infection. Interestingly, only VSV infection relied on Lgr4, whereas infections with Newcastle disease virus, influenza A virus (A/WSN/33), and herpes simplex virus were unaffected by Lgr4 status. Of note, assays of virus entry, cell ELISA, immunoprecipitation, and surface plasmon resonance indicated that VSV bound susceptible cells via the Lgr4 extracellular domain. Pretreating cells with an Lgr4 antibody, soluble LGR4 extracellular domain, or R-spondin 1 blocked VSV infection by competitively inhibiting VSV binding to Lgr4. Taken together, the identification of Lgr4 as a VSV-specific host factor provides important insights into understanding VSV entry and its pathogenesis and lays the foundation for VSV-based gene therapy and viral oncolytic therapeutics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome.

PubMed

Abdurashitov, Murat A; Gonchar, Danila A; Chernukhin, Valery A; Tomilov, Victor N; Tomilova, Julia E; Schostak, Natalia G; Zatsepina, Olga G; Zelentsova, Elena S; Evgen'ev, Michael B; Degtyarev, Sergey K H

2013-11-09

Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases. Here, we applied this approach to the annotated genome of Drosophila virilis which is extremely rich in various repeats. Here we explored the combined approach to perform the restriction analysis of D. virilis DNA. This approach enabled to reveal three abundant medium-sized tandem repeats within the D. virilis genome. While the 225 bp repeats were revealed previously in intergenic non-transcribed spacers between ribosomal genes of D. virilis, two other families comprised of 154 bp and 172 bp repeats were not described. Tandem Repeats Finder search demonstrated that 154 bp and 172 bp units are organized in multiple clusters in the genome of D. virilis. Characteristically, only 154 bp repeats derived from Helitron transposon are transcribed. Using in silico digestion in combination with conventional restriction analysis and sequencing of repeated DNA fragments enabled us to isolate and characterize three highly abundant families of medium-sized repeats present in the D. virilis genome. These repeats comprise a significant portion of the genome and may have important roles in genome function and structural integrity. Therefore, we demonstrated an approach which makes possible to investigate in detail the gross arrangement and expression of medium-sized repeats basing on sequencing data even in the case of incompletely assembled and/or annotated genomes.

Tandem resonator reflectance modulator

DOEpatents

Fritz, I.J.; Wendt, J.R.

1994-09-06

A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors. 8 figs.

Viscoelastic Properties of Core-Shell-Structured, Hemicellulose-Rich Nanofibrillated Cellulose in Dispersion and Wet-Film States.

PubMed

Tanaka, Reina; Saito, Tsuguyuki; Hänninen, Tuomas; Ono, Yuko; Hakalahti, Minna; Tammelin, Tekla; Isogai, Akira

2016-06-13

We report the viscoelastic properties of core-shell-structured, hemicellulose-rich nanofibrillated cellulose (NFC) in dispersion and wet-film states. The hemicellulose-rich NFC (hemicellulose neutral sugars 23%, carboxylate 0.2 mmol g(-1)), prepared from Japanese persimmons, had a core crystallite thickness of 2.3 nm and unit fibril thickness of 4.2 nm. A carboxylate-rich NFC (hemicellulose neutral sugars 7%, carboxylate 0.9 mmol g(-1)) with crystallite and fibril widths of 2.5 and 3.3 nm, respectively, was used as a reference. The solid-concentration dependencies of the storage moduli of gel-like water dispersions of the hemicellulose-rich NFC were weaker than those of carboxylate-rich NFC, and the dispersions were loosely flocculated even at high salt concentrations and low pH values. The viscoelastic properties of wet NFC films were similar to those of their dispersions; the hemicellulose-rich NFC films were significantly less sensitive to salt concentration and pH and were soft and swollen at high salt concentrations and low pH values.

Nutritionally enriched 1,3-diacylglycerol-rich oil: Low calorie fat with hypolipidemic effects in rats.

PubMed

Prabhavathi Devi, B L A; Gangadhar, K N; Prasad, R B N; Sugasini, D; Rao, Y Poorna Chandra; Lokesh, B R

2018-05-15

An enzymatic process was developed for the preparation of a nutritionally enriched 1,3-diacylglycerol(DAG)-rich oil from a blend of refined sunflower and rice bran oils. The process involves hydrolysis of vegetable oil blend using Candida cylindracea followed by esterification with glycerol using Lipozyme RM1M. The resultant DAG-rich oil contains 84% of DAG (66% of 1,3-DAG, 18% of 1,2-DAG) and 16% of triacylglycerol (TAG) along with micro nutrients like γ-oryzanol, tocotrienols, tocopherols and phytosterols. Nutritional studies of the DAG-rich oil were conducted in Wistar rats and compared with sunflower oil (SFO). The calorific value of the DAG-rich oil was estimated to be 6.45 Kcals/g as against 9.25 Kcals/g for SFO. The serum and liver cholesterol and TAG levels in rats fed with 1,3-DAG-rich oil were found to be significantly reduced as compared to rats fed diet containing SFO. We conclude that 1,3-DAG-rich oil is a low calorie fat and exhibits hypolipidemic effects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tandem Repeat Proteins Inspired By Squid Ring Teeth

NASA Astrophysics Data System (ADS)

Pena-Francesch, Abdon

Proteins are large biomolecules consisting of long chains of amino acids that hierarchically assemble into complex structures, and provide a variety of building blocks for biological materials. The repetition of structural building blocks is a natural evolutionary strategy for increasing the complexity and stability of protein structures. However, the relationship between amino acid sequence, structure, and material properties of protein systems remains unclear due to the lack of control over the protein sequence and the intricacies of the assembly process. In order to investigate the repetition of protein building blocks, a recently discovered protein from squids is examined as an ideal protein system. Squid ring teeth are predatory appendages located inside the suction cups that provide a strong grasp of prey, and are solely composed of a group of proteins with tandem repetition of building blocks. The objective of this thesis is the understanding of sequence, structure and property relationship in repetitive protein materials inspired in squid ring teeth for the first time. Specifically, this work focuses on squid-inspired structural proteins with tandem repeat units in their sequence (i.e., repetition of alternating building blocks) that are physically cross-linked via beta-sheet structures. The research work presented here tests the hypothesis that, in these systems, increasing the number of building blocks in the polypeptide chain decreases the protein network defects and improves the material properties. Hence, the sequence, nanostructure, and properties (thermal, mechanical, and conducting) of tandem repeat squid-inspired protein materials are examined. Spectroscopic structural analysis, advanced materials characterization, and entropic elasticity theory are combined to elucidate the structure and material properties of these repetitive proteins. This approach is applied not only to native squid proteins but also to squid-inspired synthetic polypeptides

Controlling the Morphology of BDTT-DPP-Based Small Molecules via End-Group Functionalization for Highly Efficient Single and Tandem Organic Photovoltaic Cells.

PubMed

Kim, Ji-Hoon; Park, Jong Baek; Yang, Hoichang; Jung, In Hwan; Yoon, Sung Cheol; Kim, Dongwook; Hwang, Do-Hoon

2015-11-04

A series of narrow-band gap, π-conjugated small molecules based on diketopyrrolopyrrole (DPP) electron acceptor units coupled with alkylthienyl-substituted-benzodithiophene (BDTT) electron donors were designed and synthesized for use as donor materials in solution-processed organic photovoltaic cells. In particular, by end-group functionalization of the small molecules with fluorine derivatives, the nanoscale morphologies of the photoactive layers of the photovoltaic cells were successfully controlled. The influences of different fluorine-based end-groups on the optoelectronic and morphological properties, carrier mobilities, and the photovoltaic performances of these materials were investigated. A high power conversion efficiency (PCE) of 6.00% under simulated solar light (AM 1.5G) illumination has been achieved for organic photovoltaic cells based on a small-molecule bulk heterojunction system consisting of a trifluoromethylbenzene (CF3) end-group-containing oligomer (BDTT-(DPP)2-CF3) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor. As a result, the introduction of CF3 end-groups has been found to enhance both the short circuit current density (JSC) and fill factor (FF). A tandem photovoltaic device comprising an inverted BDTT-(DPP)2-CF3:PC71BM cell and a poly(3-hexylthiophene) (P3HT):indene-C60-bisadduct (IC60BA)-based cell as the top and bottom cell components, respectively, showed a maximum PCE of 8.30%. These results provide valuable guidelines for the rational design of conjugated small molecules for applications in high-performance organic photovoltaic cells. Furthermore, to the best of our knowledge, this is the first report on the design of fluorine-functionalized BDTT-DPP-based small molecules, which have been shown to be a viable candidate for use in inverted tandem cells.

Better load-weight distribution is needed for tandem-axle logging trucks

Treesearch

John E. Baumgras

1976-01-01

To determine the GVW and axle weights of tandem-axle logging trucks hauling into two West Virginia sawmills, 543 truckloads of hardwood sawlogs were weighed. The results showed that less than 2 percent of the truckloads exceeded the 48,000 pound GVW limit. While 58 percent of the truckloads exceeded the 32,000 pound tandem-axle weight limit, the front-axle weights...

Flexible and fragmentable tandem photosensitive nanocrystal skins

NASA Astrophysics Data System (ADS)

Akhavan, S.; Uran, C.; Bozok, B.; Gungor, K.; Kelestemur, Y.; Lesnyak, V.; Gaponik, N.; Eychmüller, A.; Demir, H. V.

2016-02-01

We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of single monolayers of colloidal water-soluble CdTe and CdHgTe nanocrystals (NCs) in adjacent junctions on a Kapton polymer tape. Owing to the usage of a single NC layer in each junction, noise generation was significantly reduced while keeping the resulting PNS films considerably transparent. In each junction, photogenerated excitons are dissociated at the interface of the semi-transparent Al electrode and the NC layer, with holes migrating to the contact electrode and electrons trapped in the NCs. As a result, the tandem PNSs lead to an open-circuit photovoltage buildup equal to the sum of those of the two single junctions, exhibiting a total voltage buildup of 128.4 mV at an excitation intensity of 75.8 μW cm-2 at 350 nm. Furthermore, we showed that these flexible PNSs could be bent over 3.5 mm radius of curvature and cut out in arbitrary shapes without damaging the operation of individual parts and without introducing any significant loss in the total sensitivity. These findings indicate that the NC skins are promising as building blocks to make low-cost, flexible, large-area UV/visible sensing platforms with highly efficient full-spectrum conversion.We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of

Caspofungin Treatment of Aspergillus fumigatus Results in ChsG-Dependent Upregulation of Chitin Synthesis and the Formation of Chitin-Rich Microcolonies

PubMed Central

Walker, Louise A.; Lee, Keunsook K.; Munro, Carol A.

2015-01-01

Treatment of Aspergillus fumigatus with echinocandins such as caspofungin inhibits the synthesis of cell wall β-1,3-glucan, which triggers a compensatory stimulation of chitin synthesis. Activation of chitin synthesis can occur in response to sub-MICs of caspofungin and to CaCl2 and calcofluor white (CFW), agonists of the protein kinase C (PKC), and Ca2+-calcineurin signaling pathways. A. fumigatus mutants with the chs gene (encoding chitin synthase) deleted (ΔAfchs) were tested for their response to these agonists to determine the chitin synthase enzymes that were required for the compensatory upregulation of chitin synthesis. Only the ΔAfchsG mutant was hypersensitive to caspofungin, and all other ΔAfchs mutants tested remained capable of increasing their chitin content in response to treatment with CaCl2 and CFW and caspofungin. The resulting increase in cell wall chitin content correlated with reduced susceptibility to caspofungin in the wild type and all ΔAfchs mutants tested, with the exception of the ΔAfchsG mutant, which remained sensitive to caspofungin. In vitro exposure to the chitin synthase inhibitor, nikkomycin Z, along with caspofungin demonstrated synergistic efficacy that was again AfChsG dependent. Dynamic imaging using microfluidic perfusion chambers demonstrated that treatment with sub-MIC caspofungin resulted initially in hyphal tip lysis. However, thickened hyphae emerged that formed aberrant microcolonies in the continued presence of caspofungin. In addition, intrahyphal hyphae were formed in response to echinocandin treatment. These in vitro data demonstrate that A. fumigatus has the potential to survive echinocandin treatment in vivo by AfChsG-dependent upregulation of chitin synthesis. Chitin-rich cells may, therefore, persist in human tissues and act as the focus for breakthrough infections. PMID:26169407

A Silicon–Singlet Fission Tandem Solar Cell Exceeding 100% External Quantum Efficiency with High Spectral Stability

PubMed Central

2017-01-01

After 60 years of research, silicon solar cell efficiency saturated close to the theoretical limit, and radically new approaches are needed to further improve the efficiency. The use of tandem systems raises this theoretical power conversion efficiency limit from 34% to 45%. We present the advantageous spectral stability of using voltage-matched tandem solar cells with respect to their traditional series-connected counterparts and experimentally demonstrate how singlet fission can be used to produce simple voltage-matched tandems. Our singlet fission silicon–pentacene tandem solar cell shows efficient photocurrent addition. This allows the tandem system to benefit from carrier multiplication and to produce an external quantum efficiency exceeding 100% at the main absorption peak of pentacene. PMID:28261671

INFRARED SPECTRUM OF POTASSIUM-CATIONIZED TRIETHYLPHOSPHATE GENERATED USING TANDEM MASS SPECTROMETRY AND INFRARED MULTIPLE PHOTON DISSOCIATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gary S. Groenewold; Christopher M. Leavitt; Ryan P. Dain

2009-09-01

Tandem mass spectrometry and wavelength selective infrared photodissociation was used to generate an infrared spectrum of gas-phase triethylphosphate cationized by attachment of K+. Prominent absorptions were observed in the region of 900 to 1300 cm-1 that are characteristic of phosphate P=O and P-O-R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6-31+g(d), 6-311+g(d,p) and 6-311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which inmore » turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations.« less

Relationships between avian richness and landscape structure at multiple scales using multiple landscapes

USGS Publications Warehouse

Mitchell, M.S.; Rutzmoser, S.H.; Wigley, T.B.; Loehle, C.; Gerwin, J.A.; Keyser, P.D.; Lancia, R.A.; Perry, R.W.; Reynolds, C.J.; Thill, R.E.; Weih, R.; White, D.; Wood, P.B.

2006-01-01

Little is known about factors that structure biodiversity on landscape scales, yet current land management protocols, such as forest certification programs, place an increasing emphasis on managing for sustainable biodiversity at landscape scales. We used a replicated landscape study to evaluate relationships between forest structure and avian diversity at both stand and landscape-levels. We used data on bird communities collected under comparable sampling protocols on four managed forests located across the Southeastern US to develop logistic regression models describing relationships between habitat factors and the distribution of overall richness and richness of selected guilds. Landscape models generated for eight of nine guilds showed a strong relationship between richness and both availability and configuration of landscape features. Diversity of topographic features and heterogeneity of forest structure were primary determinants of avian species richness. Forest heterogeneity, in both age and forest type, were strongly and positively associated with overall avian richness and richness for most guilds. Road density was associated positively but weakly with avian richness. Landscape variables dominated all models generated, but no consistent patterns in metrics or scale were evident. Model fit was strong for neotropical migrants and relatively weak for short-distance migrants and resident species. Our models provide a tool that will allow managers to evaluate and demonstrate quantitatively how management practices affect avian diversity on landscapes.

A tandem mirror plasma source for hybrid plume plasma studies

NASA Technical Reports Server (NTRS)

Yang, T. F.; Chang, F. R.; Miller, R. H.; Wenzel, K. W.; Krueger, W. A.

1985-01-01

A tandem mirror device to be considered as a hot plasma source for the hybrid plume rocket concept is discussed. The hot plamsa from this device is injected into an exhaust duct, which will interact with an annular hypersonic layer of neutral gas. The device can be used to study the dynamics of the hybrid plume, and to verify the numerical predictions obtained with computer codes. The basic system design is also geared towards low weight and compactness, and high power density at the exhaust. The basic structure of the device consists of four major subsystems: (1) an electric power supply; (2) a low temperature, high density plasma gun, such as a stream gun, an MPD source or gas cell; (3) a power booster in the form of a tandem mirror machine; and (4) an exhaust nozzle arrangement. The configuration of the tandem mirror section is shown.

Impeller tandem blade study with grid embedding for local grid refinement

NASA Technical Reports Server (NTRS)

Bache, George

1992-01-01

Flow non-uniformity at the discharge of high power density impellers can result in significant unsteady interactions between impeller blades and downstream diffuser vanes. These interactions result in degradation of both performance and pump reliability. The MSFC Pump Technology Team has recognized the importance of resolving this problem and has thus initiated the development and testing of a high head coefficient impeller. One of the primary goals of this program is to improve impeller performance and discharge flow uniformity. The objective of the present work is complimentary. Flow uniformity and performance gains were sought through the application of a tandem blade arrangement. The approach adopted was to numerically establish flow characteristics at the impeller discharge for the baseline MSFC impeller and then parametrically evaluate tandem blade configurations. A tandem design was sought that improves both impeller performance and discharge uniformity. The Navier-Stokes solver AEROVISC was used to conduct the study. Grid embedding is used to resolve local gradients while attempting to minimize model size. Initial results indicate that significant gains in flow uniformity can be achieved through the tandem blade concept and that blade clocking rather than slot location is the primary driver for flow uniformity.

Progress in Tandem Solar Cells Based on Hybrid Organic-Inorganic Perovskites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Bo; Zheng, Xiaopeng; Bai, Yang

Owing to their high efficiency, low-cost solution-processability, and tunable bandgap, perovskite solar cells (PSCs) made of hybrid organic-inorganic perovskite (HOIP) thin films are promising top-cell candidates for integration with bottom-cells based on Si or other low-bandgap solar-cell materials to boost the power conversion efficiency (PCE) beyond the Shockley-Quiesser (S-Q) limit. In this review, recent progress in such tandem solar cells based on the emerging PSCs is summarized and reviewed critically. Notable achievements for different tandem solar cell configurations including mechanically-stacked, optical coupling, and monolithically-integrated with PSCs as top-cells are described in detail. Highly-efficient semitransparent PSC top-cells with high transmittance inmore » near-infrared (NIR) region are critical for tandem solar cells. Different types of transparent electrodes with high transmittance and low sheet-resistance for PSCs are reviewed, which presents a grand challenge for PSCs. The strategies to obtain wide-bandgap PSCs with good photo-stability are discussed. In conclusion, the PCE reduction due to reflection loss, parasitic absorption, electrical loss, and current mismatch are analyzed to provide better understanding of the performance of PSC-based tandem solar cells.« less

Progress in Tandem Solar Cells Based on Hybrid Organic-Inorganic Perovskites

DOE PAGES

Chen, Bo; Zheng, Xiaopeng; Bai, Yang; ...

2017-03-06

Owing to their high efficiency, low-cost solution-processability, and tunable bandgap, perovskite solar cells (PSCs) made of hybrid organic-inorganic perovskite (HOIP) thin films are promising top-cell candidates for integration with bottom-cells based on Si or other low-bandgap solar-cell materials to boost the power conversion efficiency (PCE) beyond the Shockley-Quiesser (S-Q) limit. In this review, recent progress in such tandem solar cells based on the emerging PSCs is summarized and reviewed critically. Notable achievements for different tandem solar cell configurations including mechanically-stacked, optical coupling, and monolithically-integrated with PSCs as top-cells are described in detail. Highly-efficient semitransparent PSC top-cells with high transmittance inmore » near-infrared (NIR) region are critical for tandem solar cells. Different types of transparent electrodes with high transmittance and low sheet-resistance for PSCs are reviewed, which presents a grand challenge for PSCs. The strategies to obtain wide-bandgap PSCs with good photo-stability are discussed. In conclusion, the PCE reduction due to reflection loss, parasitic absorption, electrical loss, and current mismatch are analyzed to provide better understanding of the performance of PSC-based tandem solar cells.« less

Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

ERIC Educational Resources Information Center

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

Determination of mycotoxins in plant-based beverages using QuEChERS and liquid chromatography-tandem mass spectrometry.

PubMed

Miró-Abella, Eugènia; Herrero, Pol; Canela, Núria; Arola, Lluís; Borrull, Francesc; Ras, Rosa; Fontanals, Núria

2017-08-15

A method was developed for the simultaneous determination of 11 mycotoxins in plant-based beverage matrices, using a QuEChERS extraction followed by ultra-high performance liquid chromatography coupled to tandem mass spectrometry detection (UHPLC-(ESI)MS/MS). This multi-mycotoxin method was applied to analyse plant-based beverages such as soy, oat and rice. QuEChERS extraction was applied obtaining suitable extraction recoveries between 80 and 91%, and good repeatability and reproducibility values. Method Quantification Limits were between 0.05μgL -1 (for aflatoxin G 1 and aflatoxin B 1 ) and 15μgL -1 (for deoxynivalenol and fumonisin B 2 ). This is the first time that plant-based beverages have been analysed, and certain mycotoxins, such as deoxynivalenol, aflatoxin B 1 , aflatoxin B 2 , aflatoxin G 1 , aflatoxin G 2 , ochratoxin A, T-2 toxin and zearalenone, were found in the analysed samples, and some of them quantified between 0.1μgL -1 and 19μgL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid determination of yunaconitine and related alkaloids in aconites and aconite-containing drugs by ultra high-performance liquid chromatography-tandem mass spectrometry.

PubMed

Song, Long; Zhang, Hong; Liu, Xin; Zhao, Zhi-Li; Chen, Shi-Lin; Wang, Zheng-Tao; Xu, Hong-Xi

2012-12-01

Yunaconitine (YAC) is a toxic aconite alkaloid that is considered to be a hidden aconite poison since it is frequently found in body fluids from aconite poisoning patients, but has not been well studied in commonly used herbal drugs. In this paper, a rapid and sensitive ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) detection combined with microwave-assisted extraction (MAE) was developed for high throughput simultaneous determination of YAC and six other toxic aconite alkaloids in 31 samples of crude, processed aconites and aconite-containing drugs. The optimized method showed excellent linearity, precision, accuracy and recovery for all target compounds with short run time. YAC was detected in some samples with contents from 0.015 to 10.41 mg/g. This is the first report on the determination of YAC in Radix Aconiti, Radix Aconiti Kusnezoffii and aconite-containing drugs. This newly developed method facilitates the rapid screening of YAC and related toxic aconite alkaloids and allows YAC to be used as a chemical marker for the quality control of aconites and aconite-containing drugs. Copyright © 2012 John Wiley & Sons, Ltd.

An approach for configuring space photovoltaic tandem arrays based on cell layer performance

NASA Technical Reports Server (NTRS)

Flora, C. S.; Dillard, P. A.

1991-01-01

Meeting solar array performance goals of 300 W/Kg requires use of solar cells with orbital efficiencies greater than 20 percent. Only multijunction cells and cell layers operating in tandem produce this required efficiency. An approach for defining solar array design concepts that use tandem cell layers involve the following: transforming cell layer performance at standard test conditions to on-orbit performance; optimizing circuit configuration with tandem cell layers; evaluating circuit sensitivity to cell current mismatch; developing array electrical design around selected circuit; and predicting array orbital performance including seasonal variations.

Modeling the Performance Limitations and Prospects of Perovskite/Si Tandem Solar Cells under Realistic Operating Conditions

PubMed Central

2017-01-01

Perovskite/Si tandem solar cells have the potential to considerably out-perform conventional solar cells. Under standard test conditions, perovskite/Si tandem solar cells already outperform the Si single junction. Under realistic conditions, however, as we show, tandem solar cells made from current record cells are hardly more efficient than the Si cell alone. We model the performance of realistic perovskite/Si tandem solar cells under real-world climate conditions, by incorporating parasitic cell resistances, nonradiative recombination, and optical losses into the detailed-balance limit. We show quantitatively that when optimizing these parameters in the perovskite top cell, perovskite/Si tandem solar cells could reach efficiencies above 38% under realistic conditions, even while leaving the Si cell untouched. Despite the rapid efficiency increase of perovskite solar cells, our results emphasize the need for further material development, careful device design, and light management strategies, all necessary for highly efficient perovskite/Si tandem solar cells. PMID:28920081

Modeling the Performance Limitations and Prospects of Perovskite/Si Tandem Solar Cells under Realistic Operating Conditions.

PubMed

Futscher, Moritz H; Ehrler, Bruno

2017-09-08

Perovskite/Si tandem solar cells have the potential to considerably out-perform conventional solar cells. Under standard test conditions, perovskite/Si tandem solar cells already outperform the Si single junction. Under realistic conditions, however, as we show, tandem solar cells made from current record cells are hardly more efficient than the Si cell alone. We model the performance of realistic perovskite/Si tandem solar cells under real-world climate conditions, by incorporating parasitic cell resistances, nonradiative recombination, and optical losses into the detailed-balance limit. We show quantitatively that when optimizing these parameters in the perovskite top cell, perovskite/Si tandem solar cells could reach efficiencies above 38% under realistic conditions, even while leaving the Si cell untouched. Despite the rapid efficiency increase of perovskite solar cells, our results emphasize the need for further material development, careful device design, and light management strategies, all necessary for highly efficient perovskite/Si tandem solar cells.

Monolithic tandem solar cell

DOEpatents

Wanlass, M.W.

1994-06-21

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. 9 figs.

Monolithic tandem solar cell

DOEpatents

Wanlass, Mark W.

1994-01-01

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched.

Determination of total mercury in seafood and other protein-rich products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Landi, S.; Fagioli, F.; Locatelli, C.

1992-11-01

A previously developed wet-digestion method for the determination of total mercury in plants by cold vapor atomic absorption spectroscopy (CVAAS) was extended to the analysis of seafood and other products rich in proteins. Oxidation of matrixes is accomplished by K{sub 2}Cr{sub 2}O{sub 7} in the presence of diluted H{sub 2}SO{sub 4}; a simple air condenser is used to reflux vapors released from the boiling mixture. The original procedure (A) and 2 modifications (B and C), which differ with respect to the mode of acidification and/or digestion time and the types of condensers used, were compared for precision and accuracy bymore » means of National Institute of Standards and Technology Research Material 50 Albacore Tuna and proved to be reliable (Hg present, 0.95{plus_minus}0.1 {mu}g/g; Hg found, 0.97 {plus_minus} 0.029 {mu}g/g [A], 0.98 {plus_minus} 0.018 {mu}g/g [B], and 0.94 {plus_minus} 0.025 {mu}g/g [C]). The modified procedures were tested further in Hg recovery experiments on a variety of biological matrixes with different spiking substances and again showed good analytical characteristics (overall average recoveries = 98 {plus_minus} 5.1% for seafood and 100 {plus_minus} 3.6 for protein-rich baby foods). 22 refs., 1 fig., 5 tabs.« less

Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

NASA Astrophysics Data System (ADS)

Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

2011-05-01

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

Application of response surface methodology to vortex-assisted dispersive liquid-liquid extraction for the determination of nicotine and cotinine in urine by gas chromatography-tandem mass spectrometry.

PubMed

Yuan, Yue; Wang, Yan; Yang, Mingqi; Xu, Yicong; Chen, Weina; Zou, Xiaoli; Zheng, Bo

2018-05-01

A method of vortex-assisted dispersive liquid-liquid extraction coupled with gas chromatography and tandem mass spectrometry for the determination of nicotine and cotinine in urine was developed. Response surface methodology was applied to obtain the optimum extraction conditions. In this method, Plackett-Burman design was utilized to evaluate the impact of five selected factors on pretreatment procedure. Then, three main factors were optimized using a Box-Behnken design. The optimized method showed good linearities at 1-2000 μg/L with correlation coefficients of 0.9998 for nicotine and 0.9986 for cotinine. Recovery was 91.4-106 and 91.7-108% for nicotine and cotinine, respectively. The intraday relative standard derivations of determination were 1.47-4.06% for nicotine and 0.41-3.16% for cotinine, and interday relative standard derivations were 3.03-6.70% for nicotine and 1.64-6.38% for cotinine. The method detection limits for nicotine and cotinine were 0.33 and 0.34 μg/L, respectively. A total of 87 urine samples from smokers and nonsmokers were tested with the proposed method. Urinary nicotine and cotinine were 23.0-6.67 × 10 3 and 18.4-4.17 × 10 3  μg/(g·cr) for smokers and 1.31-286 and 1.39-131 μg/(g·cr) for nonsmokers, respectively. The method is sensitive, suitable and reliable for the determination of nicotine and cotinine in urine and meets the requirements for evaluating short-term tobacco exposure. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

47 CFR 69.713 - Common line, traffic-sensitive, and tandem-switched transport services.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-switched transport services. 69.713 Section 69.713 Telecommunication FEDERAL COMMUNICATIONS COMMISSION..., traffic-sensitive, and tandem-switched transport services. (a) Scope. This paragraph governs requests for...)(2) of this chapter. (3) The traffic-sensitive components of tandem-switched transport services, as...

47 CFR 69.713 - Common line, traffic-sensitive, and tandem-switched transport services.

Code of Federal Regulations, 2011 CFR

2011-10-01

...-switched transport services. 69.713 Section 69.713 Telecommunication FEDERAL COMMUNICATIONS COMMISSION..., traffic-sensitive, and tandem-switched transport services. (a) Scope. This paragraph governs requests for...)(2) of this chapter. (3) The traffic-sensitive components of tandem-switched transport services, as...

Measurements of Short-Lived Fission Isomers

NASA Astrophysics Data System (ADS)

Finch, Sean; Bhike, Megha; Howell, Calvin; Krishichayan, Fnu; Tornow, Werner

2016-09-01

Fission yields of the short lived isomers 134mTe (T1 / 2 = 162 ns) and 136mXe (T1 / 2 = 2 . 95 μs) were measured for 235U and 238U. The isomers were detected by the γ rays associated with the decay of the isomeric states using high-purity germanium detectors. Fission was induced using both monoenergetic γ rays and neutrons. At TUNL's High-Intensity Gamma-ray Source (HI γS), γ rays of 9 and 11 MeV were produced . Monoenergetic 8 MeV neutrons were produced at TUNL's tandem accelerator laboratory. Both beams were pulsed to allow for precise time-gated spectroscopy of both prompt and delayed γ rays following fission. This technique offers a non-destructive probe of special nuclear materials that is sensitive to the isotopic identity of the fissile material.

Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmer, Nicholas J., E-mail: nic@cryst.bioc.cam.ac.uk; King, Jerry D.; Department of Veterinary Medicine, Cambridge CB3 0ES

2007-08-01

The expression, purification, and crystallisation of the short-chain dehydrogenases WbmF, WbmG and WbmH from B. bronchiseptica are described. Native diffraction data to 1.5, 2.0, and 2.2 Å were obtained for the three proteins, together with complexes with nucleotides. The short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica were cloned into Escherichia coli expression vectors, overexpressed and purified to homogeneity. Crystals of all three wild-type enzymes were obtained using vapour-diffusion crystallization with high-molecular-weight PEGs as a primary precipitant at alkaline pH. Some of the crystallization conditions permitted the soaking of crystals with cofactors and nucleotides or nucleotide sugars, whichmore » are possible substrate compounds, and further conditions provided co-complexes of two of the proteins with these compounds. The crystals diffracted to resolutions of between 1.50 and 2.40 Å at synchrotron X-ray sources. The synchrotron data obtained were sufficient to determine eight structures of the three enzymes in complex with a variety of cofactors and substrate molecules.« less

Studies of the Lateral-Directional Flying Qualities of a Tandem Helicopter in Forward Flight

NASA Technical Reports Server (NTRS)

Amer, Kenneth B; Tapscott, Robert J

1954-01-01

An investigation of the lateral-directional flying qualities of a tandem-rotor helicopter in forward flight was undertaken to determine desirable goals for helicopter lateral-directional flying qualities and possible methods of achieving these goals in the tandem-rotor helicopter. Comparison between directional stability as measured in flight and rotor-off model tests in a wind tunnel shows qualitative agreement and, hence, indicates such wind-tunnel test, despite the absence of the rotors, to be one effective method of studying means of improving the directional stability of the tandem helicopter. Flight-test measurements of turns and oscillations, in conjunction with analytical studies, suggest possible practical methods of achieving the goals of satisfactory turn and oscillatory characteristics in the tandem helicopter.

Polymerization Behavior of Hydrophilic-Rich Phase of Dentin Adhesive

PubMed Central

Abedin, F.; Parthasarathy, R.; Misra, A.; Spencer, P.

2015-01-01

inhibition/delay of postpolymerization within 2 h. Under conditions relevant to the wet, oral environment, photoinitiator content plays an important role in the polymerization of the hydrophilic-rich phase mimic. Since the hydrophilic-rich phase is primarily water and monomethacrylate monomer (e.g., HEMA as determined previously), substantial polymerization is important to limit the potential toxic response from HEMA leaching into the surrounding tissues. PMID:25576471

Electrolytes Based on TEMPO–Co Tandem Redox Systems Outperform Single Redox Systems in Dye‐sensitized Solar Cells

PubMed Central

Cong, Jiayan; Hao, Yan; Boschloo, Gerrit

2014-01-01

Abstract A new TEMPO–Co tandem redox system with TEMPO and Co(bpy)3 2+/3+ has been investigated for the use in dye‐sensitized solar cells (DSSCs). A large open‐circuit voltage (V OC) increase, from 862 mV to 965 mV, was observed in the tandem redox system, while the short‐circuit current density (J SC) was maintained. The conversion efficiency was observed to increase from 7.1 % for cells containing the single Co(bpy)3 2+/3+ redox couple, to 8.4 % for cells containing the TEMPO–Co tandem redox system. The reason for the increase in V OC and overall efficiency is ascribed to the involvement of partial regeneration of the sensitizing dye molecules by TEMPO. This assumption can be verified through the observed much faster regeneration dynamics exhibited in the presence of the tandem system. Using the tandem redox system, the faster recombination problem of the single TEMPO redox couple is resolved and the mass‐transport of the metal‐complex‐based electrolyte is also improved. This TEMPO–Co tandem system is so far the most effienct tandem redox electrolyte reported not involving iodine. The current results show a promising future for tandem system as replacements for single redox systems in electrolytes for DSSCs. PMID:25504818

Diversification rates and species richness across the Tree of Life.

PubMed

Scholl, Joshua P; Wiens, John J

2016-09-14

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. © 2016 The Author(s).

Expression of transcription factors after short-term exposure of Arabidopsis thaliana cell cultures to hyper-g, and to simulated and sounding rocket micro-g

NASA Astrophysics Data System (ADS)

Hampp, R.; Babbick, M.

Previous microarray studies with cell cultures of Arabidopsis thaliana cv Columbia have shown responses in gene expression which were partly specific to exposure to microgravity sounding rocket experiment TEXUS In order to get access to early responses upon changes in gravitational fields we used exposure times as short as 2 min For this purpose we selected a range of genes which code for different groups of transcription factors WRKY ERF MYB MADS Samples were taken in 5-min clinorotation 2- and 3-dimensional hypergravity 8g and 2-min intervals sounding rocket experiment Amounts of transcripts were determined by quantitative RT PCR Most transcripts showed a significant transient change in content within a time frame of up to 30 min after changing the external gravitational field strength They could be grouped into 1 basic stress responses which occurred under all conditions 2 clinorotation-related effects which were either identical or opposite between 2D 60 rpm 4x10 -2 g and 3D clinorotation random positioning machine and 3 alterations specific to the microgravity exposure under sounding rocket conditions MAXUS The data are discussed in relation to gravitation-dependent signalling chains and with regard to the simulation of microgravity by means of clinorotation Supported by a grant from the Deutsches Zentrum f u r Luft- und Raumfahrt e V grant no 50 WB 0143

Controlled human malaria infection trials: How tandems of trust and control construct scientific knowledge.

PubMed

Bijker, Else M; Sauerwein, Robert W; Bijker, Wiebe E

2016-02-01

Controlled human malaria infections are clinical trials in which healthy volunteers are deliberately infected with malaria under controlled conditions. Controlled human malaria infections are complex clinical trials: many different groups and institutions are involved, and several complex technologies are required to function together. This functioning together of technologies, people, and institutions is under special pressure because of potential risks to the volunteers. In this article, the authors use controlled human malaria infections as a strategic research site to study the use of control, the role of trust, and the interactions between trust and control in the construction of scientific knowledge. The authors argue that tandems of trust and control play a central role in the successful execution of clinical trials and the construction of scientific knowledge. More specifically, two aspects of tandems of trust and control will be highlighted: tandems are sites where trust and control coproduce each other, and tandems link the personal, the technical, and the institutional domains. Understanding tandems of trust and control results in setting some agendas for both clinical trial research and science and technology studies.

Monolithic tandem solar cell

DOEpatents

Wanlass, Mark W.

1991-01-01

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, and (c) a second photoactive subcell on the first subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. The solar cell can be provided as a two-terminal device or a three-terminal device.

Effects of G-Quadruplex Topology on Electronic Transfer Integrals

PubMed Central

Sun, Wenming; Varsano, Daniele; Di Felice, Rosa

2016-01-01

G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters. We show that the electronic couplings between stacked G-tetrads strongly depend on the three-dimensional atomic structure. Furthermore, we reveal a remarkable correlation with the topology: a topology characterized by the absence of syn-anti G-G sequences can better support electronic charge transfer. On the other hand, there is no obvious correlation of the electronic coupling with usual descriptors of the helix shape. We establish a procedure to maximize the correlation with a global helix shape descriptor. PMID:28335314

Highly loaded multi-stage fan drive turbine-tandem blade configuration design

NASA Technical Reports Server (NTRS)

Evans, D. C.; Wolfmeyer, G. W.

1972-01-01

The results of the tandem blade configuration design study are reported. The three stage constant-inside-diameter turbine utilizes tandem blading in the stage two and stage three vanes and in the stage three blades. All other bladerows use plain blades. Blading detailed design is discussed, and design data are summarized. Steady-state stresses and vibratory behavior are discussed, and the results of the mechanical design analysis are presented.

The proliferation marker pKi-67 becomes masked to MIB-1 staining after expression of its tandem repeats.

PubMed

Schmidt, Mirko H H; Broll, Rainer; Bruch, Hans-Peter; Duchrow, Michael

2002-11-01

The Ki-67 antigen, pKi-67, is one of the most commonly used markers of proliferating cells. The protein can only be detected in dividing cells (G(1)-, S-, G(2)-, and M-phase) but not in quiescent cells (G(0)). The standard antibody to detect pKi-67 is MIB-1, which detects the so-called 'Ki-67 motif' FKELF in 9 of the protein's 16 tandem repeats. To investigate the function of these repeats we expressed three of them in an inducible gene expression system in HeLa cells. Surprisingly, addition of a nuclear localization sequence led to a complete absence of signal in the nuclei of MIB-1-stained cells. At the same time antibodies directed against different epitopes of pKi-67 did not fail to detect the protein. We conclude that the overexpression of the 'Ki-67 motif', which is present in the repeats, can lead to inability of MIB-1 to detect its antigen as demonstrated in adenocarcinoma tissue samples. Thereafter, in order to prevent the underestimation of Ki-67 proliferation indices in MIB-1-labeled preparations, additional antibodies (for example, MIB-21) should be used. Additionally, we could show in a mammalian two-hybrid assay that recombinant pKi-67 repeats are capable of self-associating with endogenous pKi-67. Speculating that the tandem repeats are intimately involved in its protein-protein interactions, this offers new insights in how access to these repeats is regulated by pKi-67 itself.

Low driving voltage simplified tandem organic light-emitting devices by using exciplex-forming hosts

NASA Astrophysics Data System (ADS)

Zhou, Dong-Ying; Cui, Lin-Song; Zhang, Ying-Jie; Liao, Liang-Sheng; Aziz, Hany

2014-10-01

Tandem organic light-emitting devices (OLEDs), i.e., OLEDs containing multiple electroluminescence (EL) units that are vertically stacked, are attracting significant interest because of their ability to realize high current efficiency and long operational lifetime. However, stacking multiple EL units in tandem OLEDs increases driving voltage and complicates fabrication process relative to their standard single unit counterparts. In this paper, we demonstrate low driving voltage tandem OLEDs via utilizing exciplex-forming hosts in the EL units instead of conventional host materials. The use of exciplex-forming hosts reduces the charge injection barriers and the trapping of charges on guest molecules, resulting in the lower driving voltage. The use of exciplex-forming hosts also allows using fewer layers, hence simpler EL configuration which is beneficial for reducing the fabrication complexity of tandem OLEDs.

Portable Tandem Mass Spectrometer Analyzer

DTIC Science & Technology

1991-07-01

The planned instrument was to be small enough to be portable in small vehicles and was to be able to use either an atmospheric pressure ion source or a...conventional electron impact/chemical ionization ion source. In order to accomplish these developments an atmospheric pressure ionization source was...developed for a compact, commercially available tandem quadrupole mass spectrometer. This ion source could be readily exchanged with the conventional

Tetracycline residues in royal jelly and honey by liquid chromatography tandem mass spectrometry: validation study according to Commission Decision 2002/657/EC.

PubMed

Giannetti, L; Longo, F; Buiarelli, F; Russo, M V; Neri, B

2010-09-01

A specific, sensitive and robust liquid chromatography tandem mass spectrometry method for determining oxytetracycline, tetracycline, chlortetracycline and doxycycline in royal jelly and honey samples is presented. Extraction of drug residues was performed by ammonium acetate buffer as extractant followed by a clean-up with metal chelate affinity chromatography and solid-phase extraction. Tetracycline analysis was performed using liquid chromatography-electrospray ionisation-tandem mass spectrometry. The presented method is the first validated for royal jelly and in accordance with the requirements set by Commission Decision 2002/657/EC. Recoveries of the methods, calculated spiking the samples at 5.0, 10.0, 20.0 and 30.0 μg kg(-1), were 79% to 90% for honey and 77% to 90% for royal jelly. The intra-day precision (RSD) ranged between 8.1% and 15.0% for honey and from 9.1% to 16.3% for royal jelly, while inter-day precision values were from 10.2% to 17.6% and from 10.6% to 18.4% respectively for honey and royal jelly. Linearity for the four analytes was calculated from 5.0 to 50.0 μg kg(-1). The decision limits (CCα) ranged from 6.2 to 6.4 μg kg(-1) and from 6.1 to 6.5 μg kg(-1) for honey and royal jelly, respectively. Detection capabilities values (CCβ) ranged between 7.2 and 7.7 μg kg(-1) and from 7.3 to 7.9 μg kg(-1) respectively for honey and royal jelly. The developed method is currently in use for confirmation of the official control analysis of honey and royal jelly samples.

Incipient microphase separation in short chain perfluoropolyether-block-poly(ethylene oxide) copolymers.

PubMed

Chintapalli, Mahati; Timachova, Ksenia; Olson, Kevin R; Banaszak, Michał; Thelen, Jacob L; Mecham, Sue J; DeSimone, Joseph M; Balsara, Nitash P

2017-06-07

Incipient microphase separation is observed by wide angle X-ray scattering (WAXS) in short chain multiblock copolymers consisting of perfluoropolyether (PFPE) and poly(ethylene oxide) (PEO) segments. Two PFPE-PEO block copolymers were studied; one with dihydroxyl end groups and one with dimethyl carbonate end groups. Despite having a low degree of polymerization (N ∼ 10), these materials exhibited significant scattering intensity, due to disordered concentration fluctuations between their PFPE-rich and PEO-rich domains. The disordered scattering intensity was fit to a model based on a multicomponent random phase approximation to determine the value of the interaction parameter, χ, and the radius of gyration, R g . Over the temperature range 30-90 °C, the values of χ were determined to be very large (∼2-2.5), indicating a high degree of immiscibility between the PFPE and PEO blocks. In PFPE-PEO, due to the large electron density contrast between the fluorinated and non-fluorinated block and the high value of χ, disordered scattering was detected at intermediate scattering angles, (q ∼ 2 nm -1 ) for relatively small polymer chains. Our ability to detect concentration fluctuations was enabled by both a relatively large value of χ and significant scattering contrast.

Tandem accelerators in Romania: Multi-tools for science, education and technology

NASA Astrophysics Data System (ADS)

Burducea, I.; GhiÅ£ǎ, D. G.; Sava, T. B.; Straticiuc, M.

2017-06-01

An educated selection of the main beam parameters - particle type, velocity and intensity, can result in a cutting-edge scalpel to remove tumors, sanitize sewage, act as a nuclear forensics detective, date an artefact, clean up air, improve a microprocessor, transmute nuclear waste, detect a counterfeit or even look into the stars. Nowadays more than particle accelerators operate worldwide in medicine, industry and basic research. For example the proton therapy market is expected to attain 1 billion US per year in 2019 with almost 330 proton therapy rooms, while the annual market for the ion implantation industry already reached 1.5 G in revenue [1,2]. A brief history of the Tandem Accelerators Complex at IFIN-HH [3] emphasizing on their applications and the physics behind the scenes, is also presented [4-6].

Interpreting the Need for Initial Support to Perform Tandem Stance Tests of Balance

PubMed Central

Brach, Jennifer S.; Perera, Subashan; Wert, David M.; VanSwearingen, Jessie M.; Studenski, Stephanie A.

2012-01-01

Background Geriatric rehabilitation reimbursement increasingly requires documented deficits on standardized measures. Tandem stance performance can characterize balance, but protocols are not standardized. Objective The purpose of this study was to explore the impact of: (1) initial support to stabilize in position and (2) maximum hold time on tandem stance tests of balance in older adults. Design A cross-sectional secondary analysis of observational cohort data was conducted. Methods One hundred seventeen community-dwelling older adults (71% female, 12% black) were assigned to 1 of 3 groups based on the need for initial support to perform tandem stance: (1) unable even with support, (2) able only with support, and (3) able without support. The able without support group was further stratified on hold time in seconds: (1) <10 (low), (2) 10 to 29, (medium), and (3) 30 (high). Groups were compared on primary outcomes (gait speed, Timed “Up & Go” Test performance, and balance confidence) using analysis of variance. Results Twelve participants were unable to perform tandem stance, 14 performed tandem stance only with support, and 91 performed tandem stance without support. Compared with the able without support group, the able with support group had statistically or clinically worse performance and balance confidence. No significant differences were found between the able with support group and the unable even with support group on these same measures. Extending the hold time to 30 seconds in a protocol without initial support eliminated ceiling effects for 16% of the study sample. Limitations Small comparison groups, use of a secondary analysis, and lack of generalizability of results were limitations of the study. Conclusions Requiring initial support to stabilize in tandem stance appears to reflect meaningful deficits in balance-related mobility measures, so failing to consider support may inflate balance estimates and confound hold time comparisons

Nuclease digestion and mass spectrometric characterization of oligodeoxyribonucleotides containing 1,2-GpG, 1,2-ApG, and 1,3-GpXpG cisplatin intrastrand cross-links.

PubMed

Williams, Renee T; Nalbandian, Jenifer N; Tu, Audrey; Wang, Yinsheng

2013-05-01

The primary mode of action for cis-diamminedichloroplatinum (II), referred to as cisplatin, toward the treatment of solid malignancies is through formation of cross-links with DNA at purine sites, especially guanines. We prepared oligodeoxyribonucleotides (ODNs) containing a 1,2-GpG, 1,2-ApG, or 1,3-GpXpG cisplatin intrastrand cross-link and the corresponding ODNs modified with (15)N2-labeled cisplatin, and characterized these ODNs with electrospray ionization mass spectrometry (ESI-MS) and tandem MS (MS/MS). We also employed LC-MS/MS to characterize the digestion products of these ODNs after treatment with a cocktail of 4 enzymes (nuclease P1, phosphodiesterases I and II, and alkaline phosphatase). 1,2-GpG was released from the ODNs as a dinucleoside monophosphate or a dinucleotide. Analyses of the digestion products of ODNs containing a 1,2-GpG cross-link on the 5' or 3' terminus revealed that the dinucleotide carries a terminal 5' phosphate. On the other hand, digestion of the 1,3-GpXpG intrastrand cross-link yielded 3 dinucleoside products with 0, 1, or 2 phosphate groups. The availability of the ODNs carrying the stable isotope-labeled lesions, MS/MS analyses of the cisplatin-modified ODNs, and the characterization of the enzymatic digestion products of these ODNs set the stage for the future LC-MS/MS quantification of the 1,2-GpG, 1,2-ApG, and 1,3-GpXpG lesions in cellular DNA. Copyright © 2012 Elsevier B.V. All rights reserved.

Nuclease Digestion and Mass Spectrometric Characterization of Oligodeoxyribonucleotides Containing 1,2-GpG, 1,2-ApG, and 1,3-GpXpG Cisplatin Intrastrand Cross-links

PubMed Central

Williams, Renee T.; Nalbandian, Jenifer; Tu, Audrey; Wang, Yinsheng

2013-01-01

Background The primary mode of action for cis-diamminedichloroplatinum (II), referred to as cisplatin, towards the treatment of solid malignancies is through formation of cross-links with DNA at purine sites, especially guanines. Methods We prepared oligodeoxyribonucleotides (ODNs) containing a 1,2-GpG, 1,2-ApG, or 1,3-GpXpG cisplatin intrastrand cross-link and the corresponding ODNs modified with 15N2-labeled cisplatin, and characterized these ODNs with electrospray ionization mass spectrometry (ESI-MS) and tandem MS (MS/MS). We also employed LC-MS/MS to characterize the digestion products of these ODNs after treatment with a cocktail of 4 enzymes (nuclease P1, phosphodiesterases I and II, and alkaline phosphatase). Results 1,2-GpG was released from the ODNs as a dinucleoside monophosphate or a dinucleotide. Analyses of the digestion products of ODNs containing a 1,2-GpG cross-link on the 5′ or 3′ terminus revealed that the dinucleotide carries a terminal 5′ phosphate. On the other hand, digestion of the 1,3-GpXpG intrastrand cross-link yielded 3 dinucleoside products with 0, 1, or 2 phosphate groups. Results The availability of the ODNs carrying the stable isotope-labeled lesions, MS/MS analyses of the cisplatin-modified ODNs, and the characterization of the enzymatic digestion products of these ODNs set the stage for the future LC-MS/MS quantification of the 1,2-GpG, 1,2-ApG, and 1,3-GpXpG lesions in cellular DNA. PMID:23266768

Characterization of Two Unique Cholesterol-Rich Lipid Particles Isolated from Human Atherosclerotic Lesions

PubMed Central

Chao, Fei-Fei; Blanchette-Mackie, E. Joan; Chen, Ya-Jun; Dickens, Benjamin F.; Berlin, Elliott; Amende, Lynn M.; Skarlatos, Sonia I.; Gamble, Wilbert; Resau, James H.; Mergner, Wolfgang T.; Kruth, Howard S.

1990-01-01

The authors' laboratory, using histochemicalmethods, previously identified two types of cholesterol-containing lipid particles in the extracellular spaces of human atherosclerotic lesions, one particle enriched in esterified cholesterol and the other particle enriched in unesterified cholesterol. The authors isolated and characterized these lipid particles. The esterified cholesterol-rich lipid particle was a small lipid droplet and differed from intracellular lipid dropletsfound in foam cells with respect to size and chemical composition. It had an esterified cholesterol core surrounded by aphospholipidunesterified cholesterol monolayer. Some aqueous spaces were seen within the particle core. Unesterified cholesterol-rich lipid particles were multilamellated, solid structures and vesicles comprised of single or multiple lamellas. The esterified cholesterol-rich particle had a density <1.01 g/ml, whereas the unesterified cholesterol-rich particle had a density between 1.03 and 1.05 g/ml. Both particles were similar in size fraction, whereas palmitate, stearate, oleate, and linoleate were predominant in the phospholipid fraction. The origins and the role of these two unusual lipid particles in vessel wall cholesterol metabolism remain to be determined. ImagesFigure 1Figure 3Figure 4Figure 5 PMID:2297045

Single-stage experimental evaluation of tandem-airfoil rotor and stator blading for compressors, part 8

NASA Technical Reports Server (NTRS)

Brent, J. A.; Clemmons, D. R.

1974-01-01

An experimental investigation was conducted with an 0.8 hub/tip ratio, single-stage, axial flow compressor to determine the potential of tandem-airfoil blading for improving the efficiency and stable operating range of compressor stages. The investigation included testing of a baseline stage with single-airfoil blading and two tandem-blade stages. The overall performance of the baseline stage and the tandem-blade stage with a 20-80% loading split was considerably below the design prediction. The other tandem-blade stage, which had a rotor with a 50-50% loading split, came within 4.5% of the design pressure rise (delta P(bar)/P(bar) sub 1) and matched the design stage efficiency. The baseline stage with single-airfoil blading, which was designed to account for the actual rotor inlet velocity profile and the effects of axial velocity ratio and secondary flow, achieved the design predicted performance. The corresponding tandem-blade stage (50-50% loading split in both blade rows) slightly exceeded the design pressure rise but was 1.5 percentage points low in efficiency. The tandem rotors tested during both phases demonstrated higher pressure rise and efficiency than the corresponding single-airfoil rotor, with identical inlet and exit airfoil angles.

Stable isotope labeling tandem mass spectrometry (SILT) to quantify protein production and clearance rates

PubMed Central

Bateman, Randall J.; Munsell, Ling Y.; Chen, Xianghong; Holtzman, David M.; Yarasheski, Kevin E.

2007-01-01

In all biological systems, protein amount is a function of the rate of production and clearance. The speed of a response to a disturbance in protein homeostasis is determined by turnover rate. Quantifying alterations in protein synthesis and clearance rates is vital to understanding disease pathogenesis (e.g., aging, inflammation). No methods exist for quantifying production and clearance rates of low abundance (femtomole) proteins in vivo. We describe a novel, mass spectrometry-based method for quantitating low abundance protein synthesis and clearance rates in vitro and in vivo in animals and humans. The utility of this method is demonstrated with amyloid-beta (Aß), an important low abundance protein involved in Alzheimer's disease pathogenesis. We used in vivo stable isotope labeling, immunoprecipitation of Aß from cerebrospinal fluid, and quantitative liquid chromatography electrospray-ionization tandem mass spectrometry (LC-ESI-tandem MS) to quantify human Aß protein production and clearance rates. The method is sensitive and specific for stable isotope labeled amino acid incorporation into CNS (± 1% accuracy). This in vivo method can be used to identify pathophysiologic changes in protein metabolism; and may serve as a biomarker for monitoring disease risk, progression, or response to novel therapeutic agents. The technique is adaptable to other macromolecules, such as carbohydrates or lipids. PMID:17383190

Conversion of raw lignocellulosic biomass into branched long-chain alkanes through three tandem steps.

PubMed

Li, Chunrui; Ding, Daqian; Xia, Qineng; Liu, Xiaohui; Wang, Yanqin

2016-07-07

Synthesis of branched long-chain alkanes from renewable biomass has attracted intensive interest in recent years, but the feedstock for this synthesis is restricted to platform chemicals. Here, we develop an effective and energy-efficient process to convert raw lignocellulosic biomass (e.g., corncob) into branched diesel-range alkanes through three tandem steps for the first time. Furfural and isopropyl levulinate (LA ester) were prepared from hemicellulose and cellulose fractions of corncob in toluene/water biphasic system with added isopropanol, which was followed by double aldol condensation of furfural with LA ester into C15 oxygenates and the final hydrodeoxygenation of C15 oxygenates into branched long-chain alkanes. The core point of this tandem process is the addition of isopropanol in the first step, which enables the spontaneous transfer of levulinic acid (LA) into the toluene phase in the form of LA ester through esterification, resulting in LA ester co-existing with furfural in the same phase, which is the basis for double aldol condensation in the toluene phase. Moreover, the acidic aqueous phase and toluene can be reused and the residues, including lignin and humins in aqueous phase, can be separated and carbonized to porous carbon materials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Approach for ochratoxin A fast screening in spices using clean-up tandem immunoassay columns with confirmation by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS).

PubMed

Goryacheva, I Yu; De Saeger, S; Lobeau, M; Eremin, S A; Barna-Vetró, I; Van Peteghem, C

2006-09-01

An approach for ochratoxin A (OTA) fast cost-effective screening based on clean-up tandem immunoassay columns was developed and optimized for OTA detection with a cut-off level of 10 microg kg(-1) in spices. Two procedures were tested and applied for OTA detection. Column with bottom detection immunolayer was optimized for OTA determination in Capsicum ssp. spices. A modified clean-up tandem immunoassay procedure with top detection immunolayer was successfully applied for all tested spices. Its main advantages were decreasing of the number of analysis steps and quantity of antibody and also minimizing of matrix effects. The total duration of the extraction and analysis was about 40 min for six samples. Chilli, red pepper, pili-pili, cayenne, paprika, nutmeg, ginger, white pepper and black pepper samples were analyzed for OTA contamination by the proposed clean-up tandem immunoassay procedures. Clean-up tandem immunoassay results were confirmed by HPLC-MS/MS with immunoaffinity column clean-up. Among 17 tested Capsicum ssp. spices, 6 samples (35%) contained OTA in a concentration exceeding the 10 microg kg(-1) limit discussed by the European Commission. All tested nutmeg (n=8), ginger (n=5), white pepper (n=7) and black pepper (n=6) samples did not contain OTA above this action level.

Managed forest landscape structure and avian species richness in the southeastern US

Treesearch

Craig Loehle; T. Bently Wigley; Scott Rutzmoser; John A. Gerwin; Patrick D. Keyser; Richard A. Lancia; Christopher J. Reynolds; Ronald E. Thill; Robert Weih; Don White; Petra Bohall Wood

2005-01-01

Forest structural features at the stand scale (e.g., snags, stem density, species composition) and habitat attributes at larger spatial scales (e.g., landscape pattern, road density) can influence biological diversity and have been proposed as indicators in sustainable forestry programs. This study investigated relationships between such factors and total richness of...

Platelet-rich therapies for musculoskeletal soft tissue injuries.

PubMed

Moraes, Vinícius Y; Lenza, Mário; Tamaoki, Marcel Jun; Faloppa, Flávio; Belloti, João Carlos

2013-12-23

95% confidence intervals. Where appropriate, data were pooled using the fixed-effect model for RR and MD, and the random-effects model for SMD. The quality of the evidence for each outcome was assessed using GRADE criteria. We included data from 19 small single centre trials (17 randomised and two quasi-randomised; 1088 participants) that compared platelet-rich therapy with placebo, autologous whole blood, dry needling or no platelet-rich therapy. These trials covered eight clinical conditions: rotator cuff tears (arthroscopic repair) (six trials); shoulder impingement syndrome surgery (one trial); elbow epicondylitis (three trials); anterior cruciate ligament (ACL) reconstruction (four trials), ACL reconstruction (donor graft site application) (two trials), patellar tendinopathy (one trial), Achilles tendinopathy (one trial) and acute Achilles rupture surgical repair (one trial). We also grouped trials into 'tendinopathies' where platelet-rich therapy (PRT) injections were the main treatment (five trials), and surgical augmentation procedures where PRT was applied during surgery (14 trials). Trial participants were mainly male, except in trials including rotator cuff tears, and elbow and Achilles tendinopathies.Three trials were judged as being at low risk of bias; the other 16 were at high or unclear risk of bias relating to selection, detection, attrition or selective reporting, or combinations of these. The methods of preparing platelet-rich plasma (PRP) varied and lacked standardisation and quantification of the PRP applied to the patient.We were able to pool data for our primary outcomes (function, pain, adverse events) for a maximum of 11 trials and 45% of participants. The evidence for all primary outcomes was judged as being of very low quality.Data assessing function in the short term (up to three months) were pooled from five trials that assessed PRT in three clinical conditions and used four different measures. These showed no significant difference

Artificial urinary sphincter revision for urethral atrophy: Comparing single cuff downsizing and tandem cuff placement.

PubMed

Linder, Brian J; Viers, Boyd R; Ziegelmann, Matthew J; Rivera, Marcelino E; Elliott, Daniel S

2017-01-01

To compare outcomes for single urethral cuff downsizing versus tandem cuff placement during artificial urinary sphincter (AUS) revision for urethral atrophy. We identified 1778 AUS surgeries performed at our institution from 1990-2014. Of these, 406 were first AUS revisions, including 69 revisions for urethral atrophy. Multiple clinical and surgical variables were evaluated for potential association with device outcomes following revision, including surgical revision strategy (downsizing a single urethral cuff versus placing tandem urethral cuffs). Of the 69 revision surgeries for urethral atrophy at our institution, 56 (82%) were tandem cuff placements, 12 (18%) were single cuff downsizings and one was relocation of a single cuff. When comparing tandem cuff placements and single cuff downsizings, the cohorts were similar with regard to age (p=0.98), body-mass index (p=0.95), prior pelvic radiation exposure (p=0.73) and length of follow-up (p=0.12). Notably, there was no difference in 3-year overall device survival compared between single cuff and tandem cuff revisions (60% versus 76%, p=0.94). Likewise, no significant difference was identified for tandem cuff placement (ref. single cuff) when evaluating the risk of any tertiary surgery (HR 0.95, 95% CI 0.32-4.12, p=0.94) or urethral erosion/device infection following revision (HR 0.79, 95% CI 0.20-5.22, p=0.77). There was no significant difference in overall device survival in patients undergoing single cuff downsizing or tandem cuff placement during AUS revision for urethral atrophy. Copyright® by the International Brazilian Journal of Urology.

Crystal structure of LGR4-Rspo1 complex: insights into the divergent mechanisms of ligand recognition by leucine-rich repeat G-protein-coupled receptors (LGRs).

PubMed

Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

2015-01-23

Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4-6) recognize R-spondin family proteins (Rspo1-4) to stimulate Wnt signaling. In this study, we successfully utilized the "hybrid leucine-rich repeat technique," which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4-6, suggesting that LGR4-6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4-6 in ligand recognition. The molecular mechanism of LGR4-6 is distinct from the two-step mechanism of group A receptors LGR1-3 and the multiple-interface binding model of group C receptors LGR7-8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

76 FR 40935 - Vertical Tandem Lifts in Marine Terminals; Extension of the Office of Management and Budget's...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-12

...] Vertical Tandem Lifts in Marine Terminals; Extension of the Office of Management and Budget's (OMB... Standard on Vertical Tandem Lifts (VTLs) in Marine Terminals (29 CFR part 1917). The collection of... on Vertical Tandem Lifts for Marine Terminals (29 CFR part 1917). OSHA is proposing to increase the...

Achieving high performance polymer tandem solar cells via novel materials design

NASA Astrophysics Data System (ADS)

Dou, Letian

Organic photovoltaic (OPV) devices show great promise in low-cost, flexible, lightweight, and large-area energy-generation applications. Nonetheless, most of the materials designed today always suffer from the inherent disadvantage of not having a broad absorption range, and relatively low mobility, which limit the utilization of the full solar spectrum. Tandem solar cells provide an effective way to harvest a broader spectrum of solar radiation by combining two or more solar cells with different absorption bands. However, for polymer solar cells, the performance of tandem devices lags behind single-layer solar cells mainly due to the lack of suitable low-bandgap polymers (near-IR absorbing polymers). In this dissertation, in order to achieve high performance, we focus on design and synthesis of novel low bandgap polymers specifically for tandem solar cells. In Chapter 3, I demonstrate highly efficient single junction and tandem polymer solar cells featuring a spectrally matched low-bandgap conjugated polymer (PBDTT-DPP: bandgap, ˜1.44 eV). The polymer has a backbone based on alternating benzodithiophene and diketopyrrolopyrrole units. A single-layer device based on the polymer provides a power conversion efficiency of ˜6%. When the polymer is applied to tandem solar cells, a power conversion efficiency of 8.62% is achieved, which was the highest certified efficiency for a polymer solar cell. To further improve this material system, in Chapter 4, I show that the reduction of the bandgap and the enhancement of the charge transport properties of the low bandgap polymer PBDTT-DPP can be accomplished simultaneously by substituting the sulfur atoms on the DPP unit with selenium atoms. The newly designed polymer PBDTT-SeDPP (Eg = 1.38 eV) shows excellent photovoltaic performance in single junction devices with PCEs over 7% and photo-response up to 900 nm. Tandem polymer solar cells based on PBDTT-SeDPP are also demonstrated with a 9.5% PCE, which are more than 10

Methane Emission and Milk Production of Dairy Cows Grazing Pastures Rich in Legumes or Rich in Grasses in Uruguay.